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Cortical Thickness Extraction
by Bunting, Emma 18 Mar '19

18 Mar '19

External Email - Use Caution Hi Freesurfer experts, I used a script created by ENIGMA to extract the cortical thickness values for 129 subjects that had undergone reconall processing. We are using these values in VBM analysis. From reading other papers, we notice that all regional volumes are usually normalised by dividing by total intracranial volumes for each subject. I’m just wondering whether the values we are extracting from our freesurfer output files have already had this normalisation applied? The script we’ve used as follows: #!/bin/bash echo 'SubjID,L_bankssts_thickavg,L_caudalanteriorcingulate_thickavg,L_caudalmiddlefrontal_thickavg,L_cuneus_thickavg,L_entorhinal_thickavg,L_fusiform_thickavg,L_inferiorparietal_thickavg,L_inferiortemporal_thickavg,L_isthmuscingulate_thickavg,L_lateraloccipital_thickavg,L_lateralorbitofrontal_thickavg,L_lingual_thickavg,L_medialorbitofrontal_thickavg,L_middletemporal_thickavg,L_parahippocampal_thickavg,L_paracentral_thickavg,L_parsopercularis_thickavg,L_parsorbitalis_thickavg,L_parstriangularis_thickavg,L_pericalcarine_thickavg,L_postcentral_thickavg,L_posteriorcingulate_thickavg,L_precentral_thickavg,L_precuneus_thickavg,L_rostralanteriorcingulate_thickavg,L_rostralmiddlefrontal_thickavg,L_superiorfrontal_thickavg,L_superiorparietal_thickavg,L_superiortemporal_thickavg,L_supramarginal_thickavg,L_frontalpole_thickavg,L_temporalpole_thickavg,L_transversetemporal_thickavg,L_insula_thickavg,R_bankssts_thickavg,R_caudalanteriorcingulate_thickavg,R_caudalmiddlefrontal_thickavg,R_cuneus_thickavg,R_entorhinal_thickavg,R_fusiform_thickavg,R_inferiorparietal_thickavg,R_inferiortemporal_thickavg,R_isthmuscingulate_thickavg,R_lateraloccipital_thickavg,R_lateralorbitofrontal_thickavg,R_lingual_thickavg,R_medialorbitofrontal_thickavg,R_middletemporal_thickavg,R_parahippocampal_thickavg,R_paracentral_thickavg,R_parsopercularis_thickavg,R_parsorbitalis_thickavg,R_parstriangularis_thickavg,R_pericalcarine_thickavg,R_postcentral_thickavg,R_posteriorcingulate_thickavg,R_precentral_thickavg,R_precuneus_thickavg,R_rostralanteriorcingulate_thickavg,R_rostralmiddlefrontal_thickavg,R_superiorfrontal_thickavg,R_superiorparietal_thickavg,R_superiortemporal_thickavg,R_supramarginal_thickavg,R_frontalpole_thickavg,R_temporalpole_thickavg,R_transversetemporal_thickavg,R_insula_thickavg,LThickness,RThickness,LSurfArea,RSurfArea,ICV' > CorticalMeasuresENIGMA_ThickAvg.csv echo 'SubjID,L_bankssts_surfavg,L_caudalanteriorcingulate_surfavg,L_caudalmiddlefrontal_surfavg,L_cuneus_surfavg,L_entorhinal_surfavg,L_fusiform_surfavg,L_inferiorparietal_surfavg,L_inferiortemporal_surfavg,L_isthmuscingulate_surfavg,L_lateraloccipital_surfavg,L_lateralorbitofrontal_surfavg,L_lingual_surfavg,L_medialorbitofrontal_surfavg,L_middletemporal_surfavg,L_parahippocampal_surfavg,L_paracentral_surfavg,L_parsopercularis_surfavg,L_parsorbitalis_surfavg,L_parstriangularis_surfavg,L_pericalcarine_surfavg,L_postcentral_surfavg,L_posteriorcingulate_surfavg,L_precentral_surfavg,L_precuneus_surfavg,L_rostralanteriorcingulate_surfavg,L_rostralmiddlefrontal_surfavg,L_superiorfrontal_surfavg,L_superiorparietal_surfavg,L_superiortemporal_surfavg,L_supramarginal_surfavg,L_frontalpole_surfavg,L_temporalpole_surfavg,L_transversetemporal_surfavg,L_insula_surfavg,R_bankssts_surfavg,R_caudalanteriorcingulate_surfavg,R_caudalmiddlefrontal_surfavg,R_cuneus_surfavg,R_entorhinal_surfavg,R_fusiform_surfavg,R_inferiorparietal_surfavg,R_inferiortemporal_surfavg,R_isthmuscingulate_surfavg,R_lateraloccipital_surfavg,R_lateralorbitofrontal_surfavg,R_lingual_surfavg,R_medialorbitofrontal_surfavg,R_middletemporal_surfavg,R_parahippocampal_surfavg,R_paracentral_surfavg,R_parsopercularis_surfavg,R_parsorbitalis_surfavg,R_parstriangularis_surfavg,R_pericalcarine_surfavg,R_postcentral_surfavg,R_posteriorcingulate_surfavg,R_precentral_surfavg,R_precuneus_surfavg,R_rostralanteriorcingulate_surfavg,R_rostralmiddlefrontal_surfavg,R_superiorfrontal_surfavg,R_superiorparietal_surfavg,R_superiortemporal_surfavg,R_supramarginal_surfavg,R_frontalpole_surfavg,R_temporalpole_surfavg,R_transversetemporal_surfavg,R_insula_surfavg,LThickness,RThickness,LSurfArea,RSurfArea,ICV' > CorticalMeasuresENIGMA_SurfAvg.csv for subj_id in $(ls -d Subj*); do #may need to change this so that it selects subjects with FS output printf "%s," "${subj_id}" >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%s," "${subj_id}" >> CorticalMeasuresENIGMA_SurfAvg.csv for side in lh.aparc.stats rh.aparc.stats; do for x in bankssts caudalanteriorcingulate caudalmiddlefrontal cuneus entorhinal fusiform inferiorparietal inferiortemporal isthmuscingulate lateraloccipital lateralorbitofrontal lingual medialorbitofrontal middletemporal parahippocampal paracentral parsopercularis parsorbitalis parstriangularis pericalcarine postcentral posteriorcingulate precentral precuneus rostralanteriorcingulate rostralmiddlefrontal superiorfrontal superiorparietal superiortemporal supramarginal frontalpole temporalpole transversetemporal insula; do printf "%g," `grep -w ${x} ${subj_id}/stats/${side} | awk '{print $5}'` >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%g," `grep -w ${x} ${subj_id}/stats/${side} | awk '{print $3}'` >> CorticalMeasuresENIGMA_SurfAvg.csv done done printf "%g," `cat ${subj_id}/stats/lh.aparc.stats | grep MeanThickness | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%g," `cat ${subj_id}/stats/rh.aparc.stats | grep MeanThickness | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%g," `cat ${subj_id}/stats/lh.aparc.stats | grep MeanThickness | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_SurfAvg.csv printf "%g," `cat ${subj_id}/stats/rh.aparc.stats | grep MeanThickness | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_SurfAvg.csv printf "%g," `cat ${subj_id}/stats/lh.aparc.stats | grep WhiteSurfArea | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%g," `cat ${subj_id}/stats/rh.aparc.stats | grep WhiteSurfArea | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%g," `cat ${subj_id}/stats/lh.aparc.stats | grep WhiteSurfArea | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_SurfAvg.csv printf "%g," `cat ${subj_id}/stats/rh.aparc.stats | grep WhiteSurfArea | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_SurfAvg.csv printf "%g" `cat ${subj_id}/stats/aseg.stats | grep IntraCranialVol | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%g" `cat ${subj_id}/stats/aseg.stats | grep IntraCranialVol | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_SurfAvg.csv echo "" >> CorticalMeasuresENIGMA_ThickAvg.csv echo "" >> CorticalMeasuresENIGMA_SurfAvg.csv done Please let me know if you need any other info, Best wishes, Emma Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Video of brain inflating from the anatomy
by Mageshwar Selvakumar 18 Mar '19

18 Mar '19

External Email - Use Caution Dear Freesurfer Community, We are working on a publication on chronic pain and for explanation purposes, we would like to show how the brain inflates from the anatomy. For this purpose, we thought a video on how inflation takes place could be interesting. I would like to know if there are some videos already made in this perspective and where it can be obtained. Looking forward to hearing from you. Thank you, Kind regards Mageshwar Selvakumar, M.Sc Department of Pharmakologische Bildgebung und Bildanalyse Friedrich Alexander Universität Erlangen Nürnberg Office: Fahrstr. 17, 91054 Erlangen Phone: + 49-9131-8522898

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Longitudinal QDEC
by AKUDJEDU, THEOPHILUS 16 Mar '19

16 Mar '19

External Email - Use Caution Dear All, I am running a longitudinal (2-time points) group cortical analysis in Freesurfer 5.3 with Qdec. After shrinking the longitudinal QDEC table into a cross-sectional form, I added a text file containing the lines MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc in the qdec directory to guide qdec to know about the newly created files (e.g. lh.long.thickness-spc...). However, it doesn't seem to be recognizing/picking up the new files or not reading the text file named Qdecrc.txt (which has the lines above. Will be glad if you could offer any help. Thanks Theo

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One Group GLM Command Line Stream: correlating thickness with cognitive scores
by Arsenije Subotic 15 Mar '19

15 Mar '19

External Email - Use Caution Dear experts, I was hoping on examining the correlation between thickness and cognition within one group only and visualizing this using the command line stream. For my analysis I was planning on using cognitive scores that are adjusted according to published norms for age, sex, and education where possible. I do not want to use the scores as a covariate however, but simply find an association if possible. I'm assuming of course that I would use one of the one group FSGD formats https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples? Thanks! Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918-6970 arsenije.subotic1(a)ucalgary.ca

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pial surface and eTIV
by Ryan Wales 15 Mar '19

15 Mar '19

External Email - Use Caution Hello, I'm using freesurfer ver 6.0.0. If there are defects with the pial surface (i.e. the pial surface does not cover all the gray matter that it should), can you also assume that the eTIV has not been estimated incorrectly, or do pial surface inaccuracies not indicate eTIV inaccuracy? I know eTIV is estimated based on the linear transform to the talairach.xfm, but I'm not sure if there's any way to determine eTIV accuracy directly. I'm quality checking my images and am curious if I should remove subjects based on poor pial surfaces or if that does not matter. Important to note, at the moment, I'm only interested in pulling hippocampal volumes and eTIV (to get relative hippocampal volumes). Similarly, would poor pial segmentation affect the reported hippocampal volumes at all? What do you recommend? Thanks, Ryan -- Ryan Wales Graduate Student Cognition and Motor Control Neuroscience Laboratory Integrative Neuroscience Psychology Department Stony Brook University E-mail: ryan.wales(a)stonybrook.edu <ryanwales(a)stonybrook.edu>

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Re: [Freesurfer] Welch's t-test for HOV violation
by Hannah CK 15 Mar '19

15 Mar '19

External Email - Use Caution Hi Doug, We actually do want the voxel-by-voxel results. Could you please give details on how we would do that? Specifically, would we need to use the command line to run the Welch's T/F or would we extract values for each voxel and put them into another software to conduct the Welch's T/F? Thank you again. Greve, Douglas N.,Ph.D. <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Thu, 14 Mar 2019 08:45:56 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> You can use mri_segstats to get whole-cortex means (use --slabel and specify the lh.cortex.label and add --id 1). You can do the same thing with the variances. The problem with doing it after mri_glmfit is that the variances will not reflect the spatial averaging over cortex. If you really just want one number for cortex, you should use mri_segstats to extract the mean values from the stack (ie, the --y input), using --avgwf. This will give you a column of numbers, one mean for each subject. Then you can process this however you want. When I first responded, I thought that you want to do this on a voxel-wise basis. doug On Thu, Mar 14, 2019 at 10:10 AM Hannah CK <hckalman(a)gmail.com> wrote: > Hi Dr. Greve, > > Sorry about that - I had followed the "Reply via email" link on the archive page instead of posting to the forum directly. > > Thank you for this response. Can extracting the means be done at the whole-brain level? If we get the means and variances for each group, I'm assuming we would need to use ROIs. Could you please clarify whether it's possible to extract means across the whole brain? > > Thank you, > Hannah > > > > > Re: [Freesurfer] Welch's t-test for HOV violation > 2019-03-13 Thread Greve, Douglas N.,Ph.D. > Hi Hannah, please include the previous correspondence so that we have context. > Also, please remember to post to the list and not to us personally. > thanks! > doug > > > > > On 3/13/19 10:52 PM, Hannah CK wrote: > > External Email - Use Caution > > Hi Dr. Greve, > > Thank you for this response. Can extracting the means be done at the > whole-brain level? If we get the means and variances for each group, I'm > assuming we would need to use ROIs. Could you please clarify whether it's > possible to extract means across the whole brain? > > Thank you, > Hannah > > > > ___ > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > Re: [Freesurfer] Welch's t-test for HOV violation > 2019-03-11 Thread Greve, Douglas N.,Ph.D. > > > I used to have this about 20 years ago, but I stopped supporting it when it did not fit cleanly into the GLM ... The shortest route is probably to do two separate analyses with mri_glmfit, one for each group. This will output means and variances for each group. Then use fscalc to compute maps of the Welch's t. > > > On 3/11/19 1:28 PM, Hannah CK wrote: > > > > External Email - Use Caution > > > > We are conducting t-test comparisons across groups in which there is a > > large discrepancy in group sizes. HOV is violated. I've searched for > > ways to run Welch's t-test in FreeSurfer (or a similar analysis that > > does not assume homogeneity of variance) but am not finding one. > > > > Could anyone please advise on how to do this? > > > > Thank you. > >

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Color scale is off
by Nillo, Ryan Michael R 15 Mar '19

15 Mar '19

External Email - Use Caution Hello FreeSurfer users, I am using FreeSurfer version 6 with the latest dev version of freeview on a Linux machine. When I load a surface into freeview with a color scale, I notice the scale does not correlate with the values in the surface. The min and max values are always some small number (e.g. 3.0 x 10^-6). This happens even if I set the threshold in the command line. To fix it, I would need to configure the surface and click “apply”. In the past, the color scale would format itself correctly without me having to go through that configure step. Example command line: freeview -f fsaverage/surf/ph.pial:overlay=lh.thickness.betas:overlay_threshold=0,0.05:overlay_method=linear -colorscale -ss lh.lateral.thickness.beta.tiff Thanks in advance, Ryan Nillo

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Matlab error in Freesurfer
by Miguel Ángel Rivas Fernández 14 Mar '19

14 Mar '19

External Email - Use Caution Dear Freesurfer experts, I am trying to run Freesurfer commands (eg. mri_ca_label) using Matlab in a Mac computer (macOS High Sierra 10.13.6 version) and I'm receiving the following error that I suspect are due to library incompatibilities: dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib mris_ca_label -aseg /Applications/freesurfer/subjects/10018/mri/aseg.mgz -seed 1234 10018 lh /Applications/freesurfer/subjects/10018/surf/lh.sphere.reg /Applications/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs /Applications/freesurfer/subjects/10018/label/lh.aparc.annot: Aborted ans = 134 I realized that this error has been previously reported <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-November/054961.…> and, as Andrew said, one of the possible solutions could be to disable the SIP (System Protection Integrity). I have disabled the SIP following the instructions indicated here <http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection…> but unfortunately Matlab continues giving the same error. How could I solve this problem?. Any help would be appreciated. Thanks in advance. Best, -- *Miguel Ángel Rivas Fernández*

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Model the FS-FAST pre-processed data with SPM
by Zhi Li 14 Mar '19

14 Mar '19

External Email - Use Caution Hello Freesurfer experts, May I know if it is possible to transform the FS-FAST pre-processed data (left surface + right surface + subcortical region) to SPM-readable format? How could I combine the three pre-processed data together and transform them back to volume-based dataset? I would like to get the confounds matrix (filtering + whitening) during model specification and estimation that I could not find in FSFAST. Hence I want to model the FS-FAST pre-processed data with SPM. Any suggestions? Many thanks and best regards, LIzhi

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Segmentation fault
by Donatienne Van Weehaeghe 14 Mar '19

14 Mar '19

External Email - Use Caution Dear, I encountered the following error when I tried to run mri_gtmpvc -- rbv: Segmentation fault (core dumped) First I performed the PET to orig registration using spmregister, secondly I tried with the registration using mri_coreg but the error remained. I also redid the segmentation step gtmseg --s $word --xcerseg without fixing the problem. Can anyone help me with this problem? The code I tried to run: #mri_gtmpvc --i SUVR_cerebellum.nii.gz --reg suv.reg.lta --psf 5 --seg /gtmseg.mgz --default-seg-merge --auto-mask 5 0.01 --rbv --o gtmpvc.output.suvrcerebellum.spmreg --no-rescale --threads 8 Kind regards Donatienne

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