Freesurfer January 2019

freesurfer@nmr.mgh.harvard.edu

119 participants
167 discussions

mni --> RAS T1
by Krieger, Donald N. 16 Jan '19

16 Jan '19

External Email - Use Caution Is there a 4x4 transformation somewhere to convert mni coordinates to RAS T1 coordinates, I.e. something comparable to the transforms provided by mri_info -tkrscanner Thanks - Don

2 1

Re: [Freesurfer] Running TRACULA
by Yendiki, Anastasia 16 Jan '19

16 Jan '19

Have you checked the registration between the structural and diffusion? The concern here would be that some of your subjects' brains could look more like bert's brain than others, and the registration could be better for the former than the latter. You would have to ensure that this doesn't introduce biases between groups (or age/gender biases) in your specific study, and therefore does not induce false group differences or accentuate any real differences. On Jan 11, 2019 9:35 AM, Ainara Gomez <ainara.ggastiasoro(a)deusto.es> wrote: External Email - Use Caution Hi Anastasia, thank you for your rapid response. Since I do not have the T1 of my subjects, I have not run the recon-all. Instead of that, I have copy-pasted the "mri" folder (including the aparc+aseg.mgz file) located in $FREESURFER_HOME/freesurfer/subjects/bert/mri into each subject's folder ($SUBJECTS_DIR/$subjectid/) so TRACULA can find all the files from Freesurfer that are needed in trac-all prep step. Thanks a lot again, Ainara El vie., 11 ene. 2019 a las 14:49, Yendiki, Anastasia (<AYENDIKI(a)mgh.harvard.edu<mailto:AYENDIKI@mgh.harvard.edu>>) escribió: Hi Ainara - What do you mean by default freesurfer files? Can you describe how you created each subject's recon-all style directory under SUBJECTS_DIR? TRACULA looks for $SUBJECTS_DIR/$subjectid/mri/aparc+aseg.mgz for each subject ID. a.y On Jan 11, 2019 8:30 AM, Ainara Gomez <ainara.ggastiasoro(a)deusto.es<mailto:ainara.ggastiasoro@deusto.es>> wrote: External Email - Use Caution Dear Freesurfer experts, I am trying to run TRACULA as a complementary analysis on a patients and healthy controls sample. I have read in the tutorial that it is assumed that FreeSurfer has already been run on all the subjects' T1-weighted data because TRACULA will use the aparc+aseg.mgz from each subject's FreeSurfer reconstruction. However, T1s of my subjects are not available for this study and I only have the diffusion images. I have run the three steps of the trac-all separately (using the default freesurfer files: aseg+aparc.mgz...) and all the processes have ended without errors. Is this correct? Is it possible to use the default freesurfer files instead of each subject's recon-all files in order to run trac-all? Thank you very much in advance, Ainara -- Ainara Gómez Gastiasoro Dpt of Methods and Experimental Psychology Neuropsychology of Severe Medical Conditions research team Faculty of Psychology and Education University of Deusto neurolab.deusto.es<http://neurolab.deusto.es/> https://twitter.com/deustoneurolab Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3268) <tel:%2B34%20944139000> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Ainara Gómez Gastiasoro Dpt of Methods and Experimental Psychology Neuropsychology of Severe Medical Conditions research team Faculty of Psychology and Education University of Deusto neurolab.deusto.es<http://neurolab.deusto.es/> https://twitter.com/deustoneurolab Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3268) <tel:%2B34%20944139000>

2 1

preproc-sess mask issue
by Dowling, Kevin Francis 15 Jan '19

15 Jan '19

Hello FreeSurfer Experts, I'm writing with a question about a potential problems that has come up in my functional analysis. I'm running FS version 5.3 on a Linux (at the Martinos Center - CentOS release 7.6.1810). I was recently running osgm WLS analyses with mri_glmfit and the --prune flag when I noticed that a large number of vertices in my surface based analysis were pruned out due to no signal (about 40% of the entire surface, see attached an example image of a group analysis that includes one of the bad subjects: pruning_issue.png). My first thought was that this result was potentially due to a poor functional/structural alignment for some subjects. However, I re-checked my functional and structural alignments, along with the quality of the recons, and they all look good. Upon further inspection, I observed similar erroneous pruning problems affecting voxels in the mni305 space (for an example see pruning_issue2.png). This issue stems from a modest number of subjects that have first level analyses with large amounts of no signal. Indeed, removing these problematic subjects from group surface based analyses resolves most of the excessive surface pruning problems. When I look at the fmcpr.siemens.nii.gz files for the runs in the problematic subjects' directories the processed functional data looks good, but when I visualize the fmcpr.siemens.sm5.mni305.nii.gz (and ...fsaverage.lh.nii.gz / ...fsaverage.rh.nii.gz) files it is clear that an inappropriate number of voxels (/vertices) have been masked out. When I look at the brain.mni305.nii.gz, brain.fsaverage.rh.nii.gz, and brain.fsaverage.lh.nii.gz masks I can see they are missing a large number of voxels/vertices that should be in the masks, which leads me to think that something may be going wrong in the lh/rh/mni305 masking/mask generation step (though brain.nii.gz and brain.e3.nii.gz masks look fine to me). I've looked through the archives and wasn't able find a similar issue discussed previously. I was therefore wondering what might be causing this mask issue (given the alignments appear to be good) and what might be the best way to go about correcting this error. Would I need to manually edit all of these masks to include the missing voxels/vertices if the automatic generation failed or is there a better solution someone might be able to suggest? My preprocessing command is: preproc-sess -s SubjectID01 -surface fsaverage lhrh -mni305 -d $SUBJECTS_DIR -fsd bold -stc siemens -fwhm 5 -per-run I would be happy to send along mask files/other files should they be of help. Thank you in advance for any suggestions you might be able to provide! Best wishes, Kevin Kevin F. Dowling Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) 617.643.3215 He / Him / His

2 2

QDEC - command not found
by Alba Castells Sánchez 15 Jan '19

15 Jan '19

External Email - Use Caution Dear freesurfer experts, we installed the last version of freesurfer dev in a centos7 system (8th january 2019) and the matlab runtime to run segmentHA_T1.sh. We could obtain all the files without problems. However, today we tried to open qdec typing qdec like we used to do with other versions without problem and the answer is "command not found". We are really surprised, we haven't found any other comment on internet and the mailing list with this same problem. We have installed the same last version in a mac and we had the same problem. qdec doesn't exist. We have checked the files .sh in Freesurfersetup and similar files in the freesurfer direcotry looking for qdec without success. HOwever, there is a direcotry called Qdec in freesurfer/matlab/lme We don't know where is our mistake. We are also considering that maybe the issue is related with the version. Is this possible? Could you help us, please? Thousand thanks

1 0

Pial and WM edits around the temporal lobes
by Stephanie Otto 14 Jan '19

14 Jan '19

External Email - Use Caution Greetings Freesurfer Team, We are working on quality checking reconstructions and there seems to be a common problem area around the temporal lobes where the white matter surface extends beyond the pial surface, or the pial surface just looks off. We know this is a difficult area to reconstruct and we aren't entirely sure how to correct for this. We want to avoid interfering with the resulting data. Can you instruct us on how we should proceed with this kind of correction (i.e. control points vs fill voxels, etc.)? If we are looking at temporal lobe structures, how much are these areas affected (or something like the grey matter volume)? Is there a standard protocol for dealing with issues such as these? Thanks for all your help and support! Best, Stephanie Otto Academic Advisor, Department of Psychology Graduate Student, Cognitive and Brain Sciences Program Mack Social Science, Room 414 University of Nevada, Reno sotto(a)nevada.unr.edu

2 1

Re: [Freesurfer] -qcache error
by Peters, Douglas G 14 Jan '19

14 Jan '19

External Email - Use Caution I am new to FS, and I am having the same error that Krishna had last year. I don't see a link to the 'lh.white.k' file in my surf folder. Has anyone resolved this problem? I can side step the error with '-qcache -measure thickness' to only process thickness files, but I'd like to be able to process all the files in my subject folders. Thanks, Doug Command line input: recon-all -s <subject> -qcache Command line output: #@# Qdec Cache preproc lh white.K fsaverage /surf mris_preproc --s <subject> --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh nsubjects = 1 ERROR: cannot find /lh.white.K recon-all -s <subject> exited with ERRORS Re: [Freesurfer] -qcache error<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj…> Douglas Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Fri, 09 Mar 2018 08:18:34 -0800<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> It was deleted but then it was created as a link. Does the link exist? ________________________________ On 3/7/18 1:33 PM, Krishna Patel wrote: Hi - I would like to do group analysis on freesurfer data that is processed with verson 6. However when I try to run recon-all -s subjid -qcache I get following error after it runs for some time and generates some of the files. ERROR: cannot find surf/lh.white.K When I look at the log file - I see that this file was deleted. See following. total integrated curvature = -1.022*4pi (-12.846) --> 2 handles ICI = 169.4, FI = 1785.3, variation=28139.036 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K Does anyone have any idea of what might be the issue here? Thanks, -Krishna ________________________________ From: Peters, Douglas G Sent: Thursday, January 10, 2019 4:55:31 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: -qcache error I am new to FS, and I am having the same error that Krishna had last year. I don't see a link to the 'lh.white.k' file in my surf folder. Has anyone resolved this problem? I can side step the error with '-qcache -measure thickness' to only process thickness files, but I'd like to be able to process all the files in my subject folders. Thanks, Doug Command line input: recon-all -s <subject> -qcache Command line output: #@# Qdec Cache preproc lh white.K fsaverage /surf mris_preproc --s <subject> --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh nsubjects = 1 ERROR: cannot find /lh.white.K recon-all -s <subject> exited with ERRORS Re: [Freesurfer] -qcache error<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj…> Douglas Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Fri, 09 Mar 2018 08:18:34 -0800<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> It was deleted but then it was created as a link. Does the link exist? ________________________________ ________________________________ On 3/7/18 1:33 PM, Krishna Patel wrote: Hi - I would like to do group analysis on freesurfer data that is processed with verson 6. However when I try to run recon-all -s subjid -qcache I get following error after it runs for some time and generates some of the files. ERROR: cannot find surf/lh.white.K When I look at the log file - I see that this file was deleted. See following. total integrated curvature = -1.022*4pi (-12.846) --> 2 handles ICI = 169.4, FI = 1785.3, variation=28139.036 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K Does anyone have any idea of what might be the issue here? Thanks, -Krishna

1 0

Tksurfer and Freeview label visualizations look different
by Anna Mynick 14 Jan '19

14 Jan '19

External Email - Use Caution Hi, I drew a collection of surface labels by hand in Tksurfer, but when I open them in Freeview to visualize them, they look incorrect. In particular, the labels in Tksurfer were drawn without any holes, but the labels in Freeview somehow got odd unintended holes (see attached images). Has anyone else run into this? For what it's worth, I drew the labels with an overlay loaded in Tksurfer, though I didn't think this would have an effect on the labels I saved. Thanks for any help, Anna tksurfer label originally drawn (purple) [cid:775863A3-49CB-4361-A9D7-B5B0745225CE@mit.edu] freeview (below, yellow) [cid:E1BB51C1-561F-4290-9AF9-DA755DAAF3ED@mit.edu]

1 0

mris_apply_reg failing for area/volume
by James Michael Roe 14 Jan '19

14 Jan '19

External Email - Use Caution ? Dear freesurfer experts I'm running the following commands to register RH area and volume files per sub to both hemispheres of a symmetrical template following Xhemi routines. The commands have already worked for many subs, but are failing to write the target file for a number of others (and all run fine without the --jac flag) #right to left mris_apply_reg \ --src $SUBJECTS_DIR/$sub/surf/rh.area \ --trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \ --streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg $SUBJECTS_DIR/${template}/surf/lh.sphere.reg \ --jac #right to right mris_apply_reg \ --src $SUBJECTS_DIR/$sub/surf/rh.area \ --trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \ --streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg $SUBJECTS_DIR/${template}/surf/rh.sphere.reg \ --jac The error is not template-specific as the output is the same using fsaverage_sym Attached is the log file. Thanks in advance! ?- James

3 12

Grey matter excluded from pial surface
by Borges Pereira Ines Isabel 14 Jan '19

14 Jan '19

External Email - Use Caution Dear FreeSurfer developers, I am trying to obtain adequate pial surface boundaries. Unfortunately, on a few subjects, some grey matter is being excluded from the pial surface, at the temporal pole. I have attempted to solve this problem by adding control points and adding voxels on the wm.gz volume, so as to have FreeSurfer first update the wm boundary and then hopefully the pial surface. As you can see on the attached images, the control points were only partially taken into account and the pial surface was not updated. It would be great to get your support in understanding why this is happening. I am using the following Freesurfer version on Centos: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Thanks! Best regards, Inês Pereira [cid:3140210C-B81A-431D-92FC-E5BD9026A4CE@ethz.ch][cid:36204321-D704-4182-A1A8-B43F8CE27A4F@ethz.ch]

2 2

GLM analysis using own average subject
by Bunting, Emma 14 Jan '19

14 Jan '19

External Email - Use Caution Hi, I’ve encountered a few issues when performing GLM using an average subject that I have created (named avgsubject.Controls2), Essentially, the glm_preproc command fails because it is now unable to find the ‘source surface reg’, which it lists as avgsubject.Controls2.sphere.reg in the linux outputs (see below). This already seems odd to me, as I would have thought this would be the target surface reg, as avgsubject.Controls2 is the target. The error occurs because it is trying to find the file within the VIPD_014/surf directory (whereby VIPD_014 is the first subject in our fsgd file). Oddly enough, the file does exist, but within the avgsubject.Controls2/surf directory instead! I was going to copy this file into all the participant’s subject/surf directories that are listed within the fsgd file, but it seems like this is not really the right way of doing it, and there must be a reason why it hasn’t ended up in the expected directories. Is there a way to edit the glm_preproc script so that it directs it to find the avgsubject.sphere.reg file within the avgsubject folder instead, or perhaps to correct the 'source surface reg' to be lh.sphere.reg (which is found within the subject/surf directory)? I’m not sure if this is related, but when looking at the fsaverage folder (where fsaverage is the average subject created by freesurfer) vs the avgsubject.Controls2 folder, I noticed the latter contains ‘reg.template.tif’ files for both hemispheres - which the fsaverage folder lacks. The other fsaverage folders created by freesurfer found within the freesurfer directory (fsaverage3, 4, 5, 6 and freesurfer_sym) do contain these tif files. It’s probably also worth noting that when I created avgsubject, it said “completed with errors” - but when I looked in the error log it didn’t tell us any information on what the errors were. This happens for all the different avgsubjects we have created. Below I describe the commands used for each step: #make_average_subject ebunting@img-140:.../MRI_data/freesurfer$ make_average_subject --out avgsubject.Controls2 --subjects VIPD_007 VIPD_015 VIPD_017 VIPD_028 VIPD_038 VIPD_068 VIPD_069 VIPD_078 VIPD_104 VIPD_105 VIPD_108 VIPD_111 VIPD_115 VIPD_117 VIPD_118 VIPD_119 VIPD_120 VIPD_126 VIPD_142 VIPD_145 VIPD_146 VIPD_160 VIPD_167 VIPD_177 VIPD_180 VIPD_193 VIPD_234 VIPD_257 VIPD_272 VIPD_274 VIPD_275 VIPD_276 VIPD_277 VIPD_280 VIPD_404 VIPD_406 VIPD_601 #n.b. this exited 'with errors'. Details of the recon-all log is attached as “avgsubject.Controls2/scripts/recon-all.log” #The linux outputs when using this command are also attached in a file named “linux outputs for making avgsubject.Controls2” #Preprocessing for GLM analysis ebunting@img-140:.../MRI_data/freesurfer$ mris_preproc --fsgd VIPD_014_SingleSubject.New.fsgd \ > --target avgsubject.Controls2 \ > --hemi lh \ > --meas thickness \ > --out lh.VIPD_014_SingleSubject.New.Controls2.thickness.00.mgh \ > nsubjects = 38 tmpdir is ./tmp.mris_preproc.984 /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer Log file is lh.VIPD_014_SingleSubject.New.Controls2.thickness.00.mris_preproc.log Fri Jan 11 10:47:34 GMT 2019 setenv SUBJECTS_DIR /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer cd /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer /var/drc/software/64bit/freesurfer/bin/mris_preproc --fsgd VIPD_014_SingleSubject.New.fsgd --target avgsubject.Controls2 --hemi lh --meas thickness --out lh.VIPD_014_SingleSubject.New.Controls2.thickness.00.mgh Linux img-140.drc.ion.ucl.ac.uk<http://drc.ion.ucl.ac.uk> 2.6.32-279.el6.x86_64 #1 SMP Wed Jun 13 18:24:36 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.984 Src lh avgsubject.Controls2.sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/38 VIPD_014 Fri Jan 11 10:47:34 GMT 2019 -------------- ----------------------- mri_surf2surf --srcsubject VIPD_014 --srchemi lh --srcsurfreg avgsubject.Controls2.sphere.reg --trgsubject avgsubject.Controls2 --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.984/VIPD_014.1.mgh --sval /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.thickness --sfmt curv --noreshape --cortex MRISread(/var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.avgsubject.Controls2.sphere.reg): could not open file Source registration surface changed to avgsubject.Controls2.sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer cd /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer mri_surf2surf --srcsubject VIPD_014 --srchemi lh --srcsurfreg avgsubject.Controls2.sphere.reg --trgsubject avgsubject.Controls2 --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.984/VIPD_014.1.mgh --sval /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.thickness --sfmt curv --noreshape --cortex sysname Linux hostname img-140.drc.ion.ucl.ac.uk<http://drc.ion.ucl.ac.uk> machine x86_64 user ebunting srcsubject = VIPD_014 srcval = /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.thickness srctype = curv trgsubject = avgsubject.Controls2 trgval = ./tmp.mris_preproc.984/VIPD_014.1.mgh trgtype = srcsurfreg = avgsubject.Controls2.sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.avgsubject.Controls2.sphere.reg No such file or directory mri_surf2surf: could not read surface /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.avgsubject.Controls2.sphere.reg No such file or directory #N.b. Outputs when compared to using fsaverage as the target: ebunting@img-140:.../MRI_data/freesurfer$ mris_preproc --fsgd VIPD_014_SingleSubject.New.fsgd \ > --target fsaverage \ > --hemi lh \ > --meas thickness \ > --out lh.VIPD_014_SingleSubject.New.thickness.00.mgh \ > nsubjects = 38 tmpdir is ./tmp.mris_preproc.27392 /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer Log file is lh.VIPD_014_SingleSubject.New.thickness.00.mris_preproc.log Thu Jan 10 16:24:36 GMT 2019 setenv SUBJECTS_DIR /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer cd /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer /var/drc/software/64bit/freesurfer/bin/mris_preproc --fsgd VIPD_014_SingleSubject.New.fsgd --target fsaverage --hemi lh --meas thickness --out lh.VIPD_014_SingleSubject.New.thickness.00.mgh Linux img-140.drc.ion.ucl.ac.uk<http://drc.ion.ucl.ac.uk> 2.6.32-279.el6.x86_64 #1 SMP Wed Jun 13 18:24:36 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.27392 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/38 VIPD_014 Thu Jan 10 16:24:36 GMT 2019 -------------- ----------------------- mri_surf2surf --srcsubject VIPD_014 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.27392/VIPD_014.1.mgh --sval /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.thickness --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer cd /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer mri_surf2surf --srcsubject VIPD_014 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.27392/VIPD_014.1.mgh --sval /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.thickness --sfmt curv --noreshape --cortex sysname Linux hostname img-140.drc.ion.ucl.ac.uk<http://drc.ion.ucl.ac.uk> machine x86_64 user ebunting srcsubject = VIPD_014 srcval = /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.27392/VIPD_014.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.sphere.reg Loading source data Reading curvature file /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.thickness Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (156736) Reverse Loop had 34296 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 138772, nTrgMulti = 25070, MnTrgMultiHits = 2.36801 nSrc121 = 123084, nSrcLost = 0, nSrcMulti = 33652, MnSrcMultiHits = 2.2303 Reading target space mask label lh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.27392/VIPD_014.1.mgh #… and this continues for each subject within the fsgd file. #the mris_surf2surf command then works as normal using: mri_surf2surf --hemi lh --s avgsubject.Controls2 --sval lh.VIPD_014_SingleSubject.New.thickness.00.mgh --fwhm 10 --cortex --tval lh.VIPD_014_SingleSubject.New.avgsubject.Controls2.thickness.10B.mgh –> THIS WORKS, BUT IT IS USING lh.VIPD_014_SingleSubject.New.thickness.00.mgh as the input file, which was created using fsaverage – so I am unsure how valid this is to use. #glm_fit command works as normal using: ebunting@img-140:.../MRI_data/freesurfer$ mri_glmfit \ > --y lh.VIPD_014_SingleSubject.New.avgsubject.Controls2.thickness.10B.mgh \ > --fsgd VIPD_014_SingleSubject.New.fsgd \ > --C SingleSubject.1,-1.mtx --C SingleSubject.1,0.mtx --C SingleSubject.0,1.mtx --C SingleSubject.0.5,0.5.mtx \ > --surf avgsubject.Controls2 lh \ > --cortex \ > --glmdir lh.VIPD_014_SingleSubject.avgsubject.Controls2.0 \ > gdfRead(): reading VIPD_014_SingleSubject.New.fsgd #n.b. output logs for both these commands are attached in case you want to examine them too ….So essentially the GLM analysis works fine, as long as the mri_preproc step is skipped. I feel unsure about the surf2surf analysis using an input file that was created using fsaverage as the target in the mri_preproc step – hence I'm trying to figure out why the mri_preproc step won't work. Any help would be greatly appreciated! Many thanks, Emma Bunting

1 0

← Newer
1
...
8
9
10
11
12
13
14
...
17
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer January 2019