Freesurfer October 2019

freesurfer@nmr.mgh.harvard.edu

111 participants
180 discussions

Cortical thickness values on a vertex base level
by Aicha Dijkshoorn 18 Nov '19

18 Nov '19

External Email - Use Caution Dear developers, For a case-control study we are comparing the cortical thickness and cortical surface area on a vertex-base level, for which we found significant differences throughout the brain. Is it possible that, in addition to the significance values (p < .05 after FDR correction) on a vertex-base level, we can include the exact thickness or surface area value (or difference) of the significant clusters on a vertex base-level between the groups. In order words, to provide some measures to highlight the size of the significant cluster or the differences in cortical thickness / cortical surface area to provide clinically useful context. For instance, a command comparable to 'voxel size' in TBSS. As this is my first time using Freesurfer any help that you could offer on this matter would be highly appreciated. Best wishes, Brigitte Dijkshoorn

2 5

FSGD file formatting for Xhemi
by Jose Graterol 11 Nov '19

11 Nov '19

External Email - Use Caution Dear Freesurfer Community, I have a question regarding the formatting of the FSGD file while doing an analysis with Xhemi. First the --y file was created as previously explained in another discussion ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63965.html) That is, mris_preproc with --xhemi and no --fsgd flag. If I understood correctly, that would create a mgh file with the following order: sub01lh, sub01rh, sub02lh, sub02rh... Then the FSGD file while running mri_glmfit would be: GroupDescriptorFile 1 Title xxx Class sub Variables var1 Input sub01lh sub var1_lh_sub01 Input sub01rh sub var1_rh_sub01 Input sub02lh sub var1_lh_sub02 Input sub02rh sub var1_rh_sub02 Would this be correct? If so, what would be the best case for specifying a variable like age? Just repeating the value 2 times? As always, thanks in advance Kind Regards José

2 11

recon-all -s SOME_SUBJECT exited with ERRORS
by Emanuel Alvaredo 07 Nov '19

07 Nov '19

External Email - Use Caution Hello FreeSurfer Developers, I am running de following command /usr/local/freesurfer/subjects/SOME_SUBJECT /usr/local/freesurfer/bin/recon-all -s SOME_SUBJECT -i /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58 - all -parallel I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. I have checked the log but I dont find de cause. 1) FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform:Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz 3) uname -a: Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thanks in advance Emanuel

2 6

Question re: Longitudinal processing stream transforms.
by Jamie Hanson 05 Nov '19

05 Nov '19

External Email - Use Caution Dear FS List, My group was trying to look at the overlap between cortical labels in the longitudinal processing stream and I had a question re: use of transform files. In brief, we followed the commands for the longitudinal processing stream, creating a "subject-specific" template for each participant ( https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing#WorkflowSu…, using FS v.6.0). We processed T1w images multiple times and now, we wanted to transform the time 1 and time 2 (native space) scans to their subject-specific template. We used the following commands-- mri_vol2vol --mov $INDIVIDUAL_SCAN_TIME1_DIR/sub-BNU_25864_001.long.sub-BNU_25864_template/mri/brain.mgz --o $INDIVIDUAL_SCAN_TIME1/brain_001_to_temp.mgz --lta $SUBJECT_SPECIFIC_TEMPLATE_DIR/mri/transforms/sub-BNU_25864_001_to_sub-BNU_25864_template.lta --targ $SUBJECT_SPECIFIC_TEMPLATE_DIR/mri/brain.mgz But when we did this for time 1 and time 2 scans, they were poorly aligned. I also used the lta file for template to 001, but again things were poorly aligned. Should we be using m3z files? Or combining different transforms? Any guidance or suggestions are deeply appreciated. Thanks much, Jamie. -- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh Personal website: jamiehanson.org

2 1

Fwd: Fw: glm error
by Amrita Bedi 01 Nov '19

01 Nov '19

External Email - Use Caution ---------- Forwarded message ---------- From: *abedi000(a)citymail.cuny.edu <abedi000(a)citymail.cuny.edu>* < abedi000(a)citymail.cuny.edu> Date: Thursday, October 31, 2019 Subject: Fw: glm error To: Amrita Bedi <amibedi273(a)gmail.com> Amrita Bedi *Biomedical Engineering - Class of 2018* *The City College of New York - CUNY* ------------------------------ *From:* abedi000(a)citymail.cuny.edu *Sent:* Thursday, October 31, 2019 12:02 PM *To:* Freesurfer(a)nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> *Subject:* glm error Hello Freesurfer developers, I ran a seed based resting stage functional analysis for 287 subjects using the isthmus of the cingulate as a seed and now have pcc.nii.gz files in each individual subject folder. I concatenated these pcc files and am trying to run an osgm but get the following error: ERROR: DOF = 0 The commands i ran for concatenating and glm are: for l in `cat sessidBOLD2`; do mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i $l/Bold/PCC_Bold1_L/bilat*/pcc.nii.gz; done mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh --cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi /FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir all_subjects_lh_ic_pcc.TR3.glmdir The mriglmfit.log gave me the following: $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_ 1to547_TR3/FSFAST cmdline mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh --cortex --label /run/media/amritabedilocal/ DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir all_subjects_lh_ic_pcc.TR3.glmdir sysname Linux hostname imaging5.vaboston.lan machine x86_64 user root FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_ 1to547_TR3/FSFAST/4D_VOLUME_OUTPUT.lh.nii.gz logyflag 0 usedti 0 labelmask /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_ 1to547_TR3/fsaverage/label/lh.cortex.label maskinv 0 glmdir all_subjects_lh_ic_pcc.TR3.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Thank you for your help.

2 7

make_average_subject error
by Maxime Perron 31 Oct '19

31 Oct '19

3 8

Discrepancy between thresholded surface and cluster labels
by Bronwyn Overs 31 Oct '19

31 Oct '19

External Email - Use Caution Dear Freesurfer mailing list, I am trying to get to the bottom of a discrepancy between two surface based images generated from the output of an LME analysis. The surfaces in row 1 of the attached image were generated by loading the four FDR significant clusters that were >100mm^2 in the cluster summary file. The surfaces in row 2 of the attached image were generated by loading the significance map generated for the same fixed effect (saved from the LME), and thresholding at the FDR corrected p -value. The question I have is why are there such large swatches of the cortical surface in the row 2 images that are labelled as log10 p = 5, when they are not included in the most significant and largest clusters that were found in the cluster summary file? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ]

2 9

Re: [Freesurfer] nuisance factors
by Georgina Angelopoulou 31 Oct '19

31 Oct '19

External Email - Use Caution Dear Douglas, Thank you once again for your reply and your help. Attached please find the fsgd file (CMTX_b.fsgd) including age row scores and the contrast file. The command line I used is the following: - mri_glmfit --y lh.CMTX_b.thickness.10.mgh --fsgd CMTX_b.fsgd --C Contrasts/age_sim.mtx --surf fsaverage lh --cortex --glmdir lh.CMTX_b_thickness.glmdir The output is the following: georgias-mbp:CMTX georgina$ mri_glmfit --y lh.CMTX_b.thickness.10.mgh --fsgd CMTX_b.fsgd --C Contrasts/age_sim.mtx --surf fsaverage lh --cortex --glmdir lh.CMTX_b_thickness.glmdir gdfRead(): reading CMTX_b.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 45.2083 12.1603 Class Means of each Continuous Variable 1 patientmale 38.7778 2 patientfemale 53.0000 3 controlmale 40.1667 4 controlfemale 51.8462 INFO: gd2mtx_method is dods Reading source surface /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX cmdline mri_glmfit.bin --y lh.CMTX_b.thickness.10.mgh --fsgd CMTX_b.fsgd --C Contrasts/age_sim.mtx --surf fsaverage lh --cortex --glmdir lh.CMTX_b_thickness.glmdir sysname Darwin hostname 192.168.1.32 machine x86_64 user georgina FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/lh.CMTX_b.thickness.10.mgh logyflag 0 usedti 0 FSGD CMTX_b.fsgd labelmask /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.CMTX_b_thickness.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.CMTX_b_thickness.glmdir Loading y from /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/lh.CMTX_b.thickness.10.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to lh.CMTX_b_thickness.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 160.248 Matrix condition is 182721 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 148239 voxels in mask Saving mask to lh.CMTX_b_thickness.glmdir/mask.mgh Reshaping mriglm->mask... search space = 73702.448371 ERROR: dimension mismatch between X and contrast Contrasts/age_sim.mtx X has 8 cols, C has 5 cols Please note that an equivalent error appears with grey matter volume and surface area. Thank you once again, Best, Georgina

2 1

PETsurfer issue
by Mackenzie Leigh Carlson 31 Oct '19

31 Oct '19

External Email - Use Caution Hello, Wondering if anyone has had issues with PETsurfer partial volume correction. When I have used it, there are large 'holes' in the white matter. I am mostly interested in the hippocampal area, which seems unaffected by these holes, but I'm not sure if I should trust the outcome enough to still use PVC maps for the hippocampus! Any help is appreciated. Thank you! I am running this: mri_gtmpvc --i SUV-30-60-float-FixedSlope.nii.gz --reg SUVtoFS.reg.lta --psf 5 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o gtmpvc.output.nopons --no-rescale -- Mackenzie L. Carlson PhD Candidate in Bioengineering | Stanford University BA Engineering Sciences | Dartmouth College (218) 269-7473

2 1

mac gcc builds
by Hoopes, Andrew 30 Oct '19

30 Oct '19

Notice to all mac FS developers, GCC builds on macOS have become increasingly difficult to maintain, mostly due to brew issues and gcc-version incompatibles with dependencies. Clang is now the "official" mac compiler for freesurfer. The external prebuilt packages (at https://surfer.nmr.mgh.harvard.edu/pub/data/fspackages/prebuilt/osx10.11-pa…) have been updated accordingly. best, Andrew

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Freesurfer October 2019