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help > RE: Setup Pipeline error: "mismatched dimensions
Aug 29, 2022 06:08 PM | Alfonso Nieto-Castanon - Boston University
RE: Setup Pipeline error: "mismatched dimensions
Hi Raoul,
Not sure, this is a bit strange, the error was reporting that your functional data had 200 scans, but from the logs it seems it had 192 scans, so perhaps those logs may not correspond to the latest preprocessing of your data?. There is also the perhaps-related issue of preprocessing your data multiple times: from the file names (e.g. swauswau5001_resting.nii) it appears that your data had been already fully preprocessed at least twice ('s' indicates smoothing, 'w' normalization, 'a' slice-timing correction, and 'u' realignment, and these letters get prepended to your file names each time you run one of those steps). I would probably recommend reimporting your original data into CONN, and running preprocessing just once (e.g. if the original input filenames are "5001_resting.nii" the fully preprocessed data will be named just "swau5001_resting.nii") and seeing whether that seems to fix this issue
Hope this helps
Alfonso
Originally posted by Raoul Hernandez:
Not sure, this is a bit strange, the error was reporting that your functional data had 200 scans, but from the logs it seems it had 192 scans, so perhaps those logs may not correspond to the latest preprocessing of your data?. There is also the perhaps-related issue of preprocessing your data multiple times: from the file names (e.g. swauswau5001_resting.nii) it appears that your data had been already fully preprocessed at least twice ('s' indicates smoothing, 'w' normalization, 'a' slice-timing correction, and 'u' realignment, and these letters get prepended to your file names each time you run one of those steps). I would probably recommend reimporting your original data into CONN, and running preprocessing just once (e.g. if the original input filenames are "5001_resting.nii" the fully preprocessed data will be named just "swau5001_resting.nii") and seeing whether that seems to fix this issue
Hope this helps
Alfonso
Originally posted by Raoul Hernandez:
Hello,
Apologies if I missed the response to this, but would you have any other suggestions given the prepocessing appears to have correctly completed.
Cheers,
R
Originally posted by Raoul Hernandez:
Apologies if I missed the response to this, but would you have any other suggestions given the prepocessing appears to have correctly completed.
Cheers,
R
Originally posted by Raoul Hernandez:
Alfonso,
Thank you. I do not get any errors with preprocessing ("Preprocessing finished correctly; Output files imported"). Here is a part of the log window. Maybe I'm overlooking something?
SPM preprocessing job
(1).spm.spatial.realignunwarp.eoptions.rtm = 0
(1).spm.spatial.realignunwarp.data.scans(1) = /mounts/charles/swauswau5001_resting.nii,9
(1).spm.spatial.realignunwarp.data.scans(2) = /mounts/charles/swauswau5001_resting.nii,10
(1).spm.spatial.realignunwarp.data.scans(191) = /mounts/charles/swauswau5001_resting.nii,199
(1).spm.spatial.realignunwarp.data.scans(192) = /mounts/charles/swauswau5001_resting.nii,200
2022-Aug-02 09:37 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Center to (0,0,0) coordinates (translation)
Performing functional Center to (0,0,0) coordinates (translation)
Importing results to CONN project
Functional centering translation x/y/z = [-0.75 19.25 -17.25] (Subject 1)
2022-Aug-02 09:39 : Functional centering translation x/y/z = [-0.75 19.25 -17.25] (Subject 16)
saved /mounts/charles/conn_project01.mat
Preparing functional Slice-Timing correction (STC; correction for inter-slice differences in acquisition time)
Performing functional Slice-Timing correction (STC; correction for inter-slice differences in acquisition time)
SPM preprocessing job
(1).spm.temporal.st.scans(1) = /mounts/charles/uswauswau5001_resting.nii,9
(1).spm.temporal.st.scans(2) = /mounts/charles/uswauswau5001_resting.nii,10
(1).spm.temporal.st.scans(191) = /mounts/charles/uswauswau5001_resting.nii,199
(1).spm.temporal.st.scans(192) = /mounts/charles/uswauswau5001_resting.nii,200
2022-Aug-02 10:30 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Outlier detection (ART-based identification of outlier scans for scrubbing)
Performing functional Outlier detection (ART-based identification of outlier scans for scrubbing)
Mapping files for session 1...:
...done
Calculating globals...:
...done
Session 1 global statistics - mean: 257.9224 stdv: 0.9133
Outlier detection: 0 identified outliers
Statistics of movement data:
x y z pitch roll yaw norm
mean 0.0020 0.0034 0.0066 0.0001 0.0001 0.0001 0.0214
stdv 0.0015 0.0026 0.0050 0.0001 0.0001 0.0000 0.0108
max 0.0073 0.0127 0.0284 0.0005 0.0004 0.0002 0.0679
Saving SPM regressor file /mounts/charles/art_regression_outliers_auswauswau5001_resting.mat and /mounts/charles/art_regression_outliers_and_movement_auswauswau5001_resting.mat
New analysis mask file saved to /mounts/charles/art_mask_auswauswau5001_resting.nii
New Voxel-wise mean file saved to /mounts/charles/art_mean_auswauswau5001_resting.nii
Importing results to CONN project
Updated 2nd-level covariate QC_ValidScans
Updated 2nd-level covariate QC_InvalidScans
Updated 2nd-level covariate QC_MaxMotion
Updated 2nd-level covariate QC_MeanMotion
Updated 2nd-level covariate QC_MaxGSchange
Updated 2nd-level covariate QC_MeanGSchange
saved /mounts/charles/conn_project01.mat
Preparing functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
Performing functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
SPM preprocessing job
(1).spm.spatial.preproc.channel.vols(1) = /mounts/charles/art_mean_auswauswau5001_resting.nii
(1).spm.spatial.preproc.channel.vols(2) = /mounts/charles/art_mean_auswauswau5002_resting.nii
(1).spm.spatial.preproc.channel.vols(15) = /mounts/charles/art_mean_auswauswau5056_resting.nii
(1).spm.spatial.preproc.channel.vols(16) = /mounts/charles/art_mean_auswauswau5058_resting.nii
(1).spm.spatial.preproc.warp.write = [1 1]
(2).spm.spatial.normalise.write.woptions.bb = [-90 -126 -72;90 90 108]
(2).spm.spatial.normalise.write.woptions.vox = [2 2 2]
(2).spm.spatial.normalise.write.subj(1).def = /mounts/charles/y_art_mean_auswauswau5001_resting.nii
(2).spm.spatial.normalise.write.subj(1).resample(1) = /mounts/charles/art_mean_auswauswau5001_resting.nii
2022-Aug-02 10:44 : (2).spm.spatial.normalise.write.subj(1).resample(2) = /mounts/charles/c1art_mean_auswauswau5001_resting.nii
(2).spm.spatial.normalise.write.subj(1).resample(195) = /mounts/charles/auswauswau5001_resting.nii,199
(2).spm.spatial.normalise.write.subj(1).resample(196) = /mounts/charles/auswauswau5001_resting.nii,200
2022-Aug-02 12:06 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
Performing functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing structural Center to (0,0,0) coordinates (translation)
Performing structural Center to (0,0,0) coordinates (translation)
Importing results to CONN project
Structural centering translation x/y/z = [-0.5 18.5 -17.5] (Subject 1)
saved /mounts/charles/conn_project01.mat
Preparing structural Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
Performing structural Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
SPM preprocessing job
(1).spm.spatial.preproc.channel.vols(1) = /mounts/charles/cwc0cwc0c5001_highres_head.nii
(1).spm.spatial.preproc.channel.vols(2) = /mounts/charles/cwc0cwc0c5002_highres_head.nii
(1).spm.spatial.preproc.channel.vols(15) = /mounts/charles/cwc0cwc0c5056_highres_head.nii
(1).spm.spatial.preproc.channel.vols(16) = /mounts/charles/cwc0cwc0c5058_highres_head.nii
(1).spm.spatial.preproc.warp.write = [1 1]
(2).spm.spatial.normalise.write.woptions.bb = [-90 -126 -72;90 90 108]
(2).spm.spatial.normalise.write.woptions.vox = [1 1 1]
(2).spm.spatial.normalise.write.subj(1).def = /mounts/charles/y_cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(1) = /mounts/charles/cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(2) = /mounts/charles/c1cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(3) = /mounts/charles/c2cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(4) = /mounts/charles/c3cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.expression = (i2+i3+i4).*i1
(3).spm.util.imcalc.input(1) = /mounts/charles/wcwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(2) = /mounts/charles/wc1cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(3) = /mounts/charles/wc2cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(4) = /mounts/charles/wc3cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.output = /mounts/charles/wc0cwc0cwc0c5001_highres_head.nii
2022-Aug-02 14:55 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Label current functional files as part of list of Secondary Datasets ("smoothed data" label)
Performing functional Label current functional files as part of list of Secondary Datasets ("smoothed data" label)
Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preprocessing finished correctly; Output files imported.
Raoul
Thank you. I do not get any errors with preprocessing ("Preprocessing finished correctly; Output files imported"). Here is a part of the log window. Maybe I'm overlooking something?
SPM preprocessing job
(1).spm.spatial.realignunwarp.eoptions.rtm = 0
(1).spm.spatial.realignunwarp.data.scans(1) = /mounts/charles/swauswau5001_resting.nii,9
(1).spm.spatial.realignunwarp.data.scans(2) = /mounts/charles/swauswau5001_resting.nii,10
(1).spm.spatial.realignunwarp.data.scans(191) = /mounts/charles/swauswau5001_resting.nii,199
(1).spm.spatial.realignunwarp.data.scans(192) = /mounts/charles/swauswau5001_resting.nii,200
2022-Aug-02 09:37 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Center to (0,0,0) coordinates (translation)
Performing functional Center to (0,0,0) coordinates (translation)
Importing results to CONN project
Functional centering translation x/y/z = [-0.75 19.25 -17.25] (Subject 1)
2022-Aug-02 09:39 : Functional centering translation x/y/z = [-0.75 19.25 -17.25] (Subject 16)
saved /mounts/charles/conn_project01.mat
Preparing functional Slice-Timing correction (STC; correction for inter-slice differences in acquisition time)
Performing functional Slice-Timing correction (STC; correction for inter-slice differences in acquisition time)
SPM preprocessing job
(1).spm.temporal.st.scans(1) = /mounts/charles/uswauswau5001_resting.nii,9
(1).spm.temporal.st.scans(2) = /mounts/charles/uswauswau5001_resting.nii,10
(1).spm.temporal.st.scans(191) = /mounts/charles/uswauswau5001_resting.nii,199
(1).spm.temporal.st.scans(192) = /mounts/charles/uswauswau5001_resting.nii,200
2022-Aug-02 10:30 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Outlier detection (ART-based identification of outlier scans for scrubbing)
Performing functional Outlier detection (ART-based identification of outlier scans for scrubbing)
Mapping files for session 1...:
...done
Calculating globals...:
...done
Session 1 global statistics - mean: 257.9224 stdv: 0.9133
Outlier detection: 0 identified outliers
Statistics of movement data:
x y z pitch roll yaw norm
mean 0.0020 0.0034 0.0066 0.0001 0.0001 0.0001 0.0214
stdv 0.0015 0.0026 0.0050 0.0001 0.0001 0.0000 0.0108
max 0.0073 0.0127 0.0284 0.0005 0.0004 0.0002 0.0679
Saving SPM regressor file /mounts/charles/art_regression_outliers_auswauswau5001_resting.mat and /mounts/charles/art_regression_outliers_and_movement_auswauswau5001_resting.mat
New analysis mask file saved to /mounts/charles/art_mask_auswauswau5001_resting.nii
New Voxel-wise mean file saved to /mounts/charles/art_mean_auswauswau5001_resting.nii
Importing results to CONN project
Updated 2nd-level covariate QC_ValidScans
Updated 2nd-level covariate QC_InvalidScans
Updated 2nd-level covariate QC_MaxMotion
Updated 2nd-level covariate QC_MeanMotion
Updated 2nd-level covariate QC_MaxGSchange
Updated 2nd-level covariate QC_MeanGSchange
saved /mounts/charles/conn_project01.mat
Preparing functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
Performing functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
SPM preprocessing job
(1).spm.spatial.preproc.channel.vols(1) = /mounts/charles/art_mean_auswauswau5001_resting.nii
(1).spm.spatial.preproc.channel.vols(2) = /mounts/charles/art_mean_auswauswau5002_resting.nii
(1).spm.spatial.preproc.channel.vols(15) = /mounts/charles/art_mean_auswauswau5056_resting.nii
(1).spm.spatial.preproc.channel.vols(16) = /mounts/charles/art_mean_auswauswau5058_resting.nii
(1).spm.spatial.preproc.warp.write = [1 1]
(2).spm.spatial.normalise.write.woptions.bb = [-90 -126 -72;90 90 108]
(2).spm.spatial.normalise.write.woptions.vox = [2 2 2]
(2).spm.spatial.normalise.write.subj(1).def = /mounts/charles/y_art_mean_auswauswau5001_resting.nii
(2).spm.spatial.normalise.write.subj(1).resample(1) = /mounts/charles/art_mean_auswauswau5001_resting.nii
2022-Aug-02 10:44 : (2).spm.spatial.normalise.write.subj(1).resample(2) = /mounts/charles/c1art_mean_auswauswau5001_resting.nii
(2).spm.spatial.normalise.write.subj(1).resample(195) = /mounts/charles/auswauswau5001_resting.nii,199
(2).spm.spatial.normalise.write.subj(1).resample(196) = /mounts/charles/auswauswau5001_resting.nii,200
2022-Aug-02 12:06 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
Performing functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing structural Center to (0,0,0) coordinates (translation)
Performing structural Center to (0,0,0) coordinates (translation)
Importing results to CONN project
Structural centering translation x/y/z = [-0.5 18.5 -17.5] (Subject 1)
saved /mounts/charles/conn_project01.mat
Preparing structural Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
Performing structural Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
SPM preprocessing job
(1).spm.spatial.preproc.channel.vols(1) = /mounts/charles/cwc0cwc0c5001_highres_head.nii
(1).spm.spatial.preproc.channel.vols(2) = /mounts/charles/cwc0cwc0c5002_highres_head.nii
(1).spm.spatial.preproc.channel.vols(15) = /mounts/charles/cwc0cwc0c5056_highres_head.nii
(1).spm.spatial.preproc.channel.vols(16) = /mounts/charles/cwc0cwc0c5058_highres_head.nii
(1).spm.spatial.preproc.warp.write = [1 1]
(2).spm.spatial.normalise.write.woptions.bb = [-90 -126 -72;90 90 108]
(2).spm.spatial.normalise.write.woptions.vox = [1 1 1]
(2).spm.spatial.normalise.write.subj(1).def = /mounts/charles/y_cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(1) = /mounts/charles/cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(2) = /mounts/charles/c1cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(3) = /mounts/charles/c2cwc0cwc0c5001_highres_head.nii
(2).spm.spatial.normalise.write.subj(1).resample(4) = /mounts/charles/c3cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.expression = (i2+i3+i4).*i1
(3).spm.util.imcalc.input(1) = /mounts/charles/wcwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(2) = /mounts/charles/wc1cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(3) = /mounts/charles/wc2cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.input(4) = /mounts/charles/wc3cwc0cwc0c5001_highres_head.nii
(3).spm.util.imcalc.output = /mounts/charles/wc0cwc0cwc0c5001_highres_head.nii
2022-Aug-02 14:55 : Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preparing functional Label current functional files as part of list of Secondary Datasets ("smoothed data" label)
Performing functional Label current functional files as part of list of Secondary Datasets ("smoothed data" label)
Importing results to CONN project
saved /mounts/charles/conn_project01.mat
Preprocessing finished correctly; Output files imported.
Raoul
Threaded View
| Title | Author | Date |
|---|---|---|
| Sascha Froelich | Apr 5, 2017 | |
| Alfonso Nieto-Castanon | Apr 5, 2017 | |
| Raoul Hernandez | Jul 28, 2022 | |
| Alfonso Nieto-Castanon | Aug 1, 2022 | |
| Raoul Hernandez | Aug 3, 2022 | |
| Raoul Hernandez | Aug 20, 2022 | |
| Alfonso Nieto-Castanon | Aug 29, 2022 | |
| Matti Gärtner | Apr 28, 2017 | |
| Sascha Froelich | Apr 11, 2017 | |