Freesurfer December 2017

freesurfer@nmr.mgh.harvard.edu

107 participants
172 discussions

Correcting defect
by shi yao wang 31 Dec '17

31 Dec '17

Dear FS experts, I am running FS 6.0. There is a error message like this. [image: Inline image 1] are there any way to modify it? thanks Lawrence Radiology Department Emory University

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Recon on resected brain
by Xiaosong He 31 Dec '17

31 Dec '17

Dear experts, I recently accidentally found that the v6.0 version of freesurfer did a nice job on brain with resection (i.e., clear resection for brain tumor or epilepsy). I am wondering was there any specific optimization done for this version? If there was, where can I found corresponding citations? Thanks all in advance and happy holidays! With kind regards. Sincerely, Xiaosong

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Left and right hemisphere aseg.mgz
by Fereshte 31 Dec '17

31 Dec '17

Dear Experts, I'd appreciate your help with this question. Are there any files which contain the left and right hemisphere segmentation of aseg.mgz separately? Thanks in advance. Regards, Fereshte

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how to estimate skull/scalp thickness
by Russell Butler 31 Dec '17

31 Dec '17

hello, i was wondering if it is possible to estimate skull/scalp thickness using freesurfer? if so does anyone know how this can be accomplished? thanks, Russell Butler

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Monte-Carlo f-test
by basile pinsard 31 Dec '17

31 Dec '17

Hi Freesurfer experts. Does mri_glmfit-sim Monte-Carlo cluster size correction is also usable for F-test? The doc says that it synthesizes a z map (I assume from a normal distribution) for computing the voxel-wise thresholds and cluster size distribution. Maybe I am wrong with my stats but I wonder if it is ok to use this null-hypothesis to a F-distributed data such as results from a F-test. Thanks! -- Basile Pinsard *PhD candidate, * Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne Universités, UPMC, INSERM, CNRS *Brain-Cognition-Behaviour Doctoral School **, *ED3C*, *UPMC, Sorbonne Universités Biomedical Sciences Doctoral School, Faculty of Medicine, Université de Montréal CRIUGM, Université de Montréal

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Monte-Carlo correction and 3-groups comparison
by Pauline Duret 31 Dec '17

31 Dec '17

Hello all, I am running a gyrification analysis between 3 groups. So I modeled my GLM like the one on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V> I was wondering if it is correct to run a Monte-Carlo correction on the results of the Main effect of group (contrast 4 on the page), which represents an F test if I am correct. I use the line mri_glmfit-sim --glmdir Results.rh.00.Groupeffectseul --cache 2 abs --cwp 0.05 --2spaces I get no sig Monte-Carlo corrected results on the main effect of group whereas I find interesting sig results in the one-by-one contrast, which is a bit surprising. Thank you for your answer. ——— lnc-autisme.umontreal.ca En apprendre plus sur l’autisme: http://grouperechercheautismemontreal.ca/Magazine.aspx <http://grouperechercheautismemontreal.ca/Magazine.aspx>

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"Normal MRI pictures"
by Gernot Ernst 31 Dec '17

31 Dec '17

I would like to analyze clincial structural MRI exams with help of Freesurfer. Is it generally possible without applying special protocols or is it completely useless? Grateful for any hints Gernot ErnstKongsberg, Norway

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Freesurfer surface to Fieldtrip SPM
by Dorothy Sincasto 31 Dec '17

31 Dec '17

Hi I've been struggling to convert a freesurfer surface into an MNI space coordinate. I tried to follow some tutorials and to play around with transformation matrices but nothing works. I have an MNI surface from freesurfer (the cvs_avg35_inMNI152) and I need to align it to the 3d MNI 152. When loading them with fieldtrip it almost matches as can be seen in the picture https://ibb.co/evkcRb I would like to apply a transformation to align the surface to the volume. For the 3d MNI I have the transformation matrix: -1 0 0 91 0 1 0 -127 0 0 1 -73 0 0 0 1 For the surface I can get the ori.mgz transformation: -1 0 0 128 0 0 1 -146 0 -1 0 148 0 0 0 1 Could someone point me out how to convert the FS surface into spm coordinates? Thank you Dorothy

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qdec question
by Giovanni de Marco 31 Dec '17

31 Dec '17

Hello, I’ve got a question concerning qdec running with freesurfer. I just downloaded the latest version of freesurfer. Before to run qdec, I read than I have to run "recon-all -s ID -all" (about 7 hours) and then recon-all -s ID -qcache (about 5'). So I tried it with one subject and everything is fine. Indeed, I got the files like *.fwhm5.fsaverage.mgh, *.fwhm10.fsaverage.mgh, *.fwhm20.fsaverage.mgh, etc... in the surf folder absolutely necessary for qdec. My question is very simple : I have already treated all my subjects (n = 45) two years ago. Today, I would like to use qdec. Do I need to restart *for each subject* all my preprocessing with recon-all -s ID -all followed by recon-all -s ID -qcache ? or Is there a routine faster to get the smoothed surfaces for each subject ? Many thank for any advice. Best wishes and happy new year. Giovanni

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Re: [Freesurfer] FreeSurfer recon-all issue
by Antonin Skoch 31 Dec '17

31 Dec '17

Dear Shadia, please check, that you really edited your recon.all, as I suggested in my previous mail. Your recon-all file is located here: /home/s1163658/freesurferv60/bin/recon-all According to your recon-all.log, there is still an ln -s command invoked (which should be replaced by cp command). It is normal that the log from new invocation of recon-all is appended to current recon-all.log. As a test, you can try to run only the step which is currently failing: recon-all -s your_subject -curvHK Also, by default, recon-all invocation does not automatically account already finished steps. To skip already successfully finished steps, you can try to run recon-all -s your_subject -make all (not sure if it works OK in v6) or explicitly list steps which need to be run: recon-all -s your_subject -curvHK -curvstats -autorecon3 Antonin Dear Antonin, Thank you for your suggestions at https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-December/055319.… . I've tried both, but the process still fails at the same point. It appears that I now am left with a recon-all log file (attached) that is double in length (run 1 ending at line 4187, and run 2 ending at 8276), both of which have started from step 1, rather than run 2 resuming from where we last stopped. Should I be adding certain flags for recon-all to resume rather than start from the beginning? The way I did it was the same as before, but without the -I flag in the second run, as suggested by the recon-all prompt. Thanks again. Shadia -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -----Original Message----- From: MIKHAEL Shadia Sent: 28 December 2017 10:12 To: 'freesurfer(a)nmr.mgh.harvard.edu' <freesurfer(a)nmr.mgh.harvard.edu> Subject: FreeSurfer recon-all issue Hello all, I'm having trouble with recon-all on a Linux server, I'm running into the following error for all of my subjects: ..... mris_curvature -w lh.white.preaparc total integrated curvature = 6.657*4pi (83.654) --> -6 handles ICI = 129.9, FI = 1309.2, variation=20703.115 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 ln: creating symbolic link `lh.white.H': Operation not supported Linux bsrv10 ..... #1 SMP Tue Nov 15 14:13:21 CST 2016 x86_64 x86_64 x86_64 GNU/Linux I've tried to create a symbolic link as suggested in https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/04047… , but I still get a message saying operation not supported ln -s /usr/local/freesurfer/subjects/fsaverage /home/s1163658/W/Cortical_analyses_for_ageing_and_dementia/NIH_Shadia ln: creating symbolic link `/home/s1163658/W/Cortical_analyses_for_ageing_and_dementia/NIH_Shadia/fsaverage': Operation not supported I've also tried to manually create the symbolic link in that last line: ln -s lh.white.preaparc.H lh.white.H But again it says operation not supported. Recon-all log: attached Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Any advice? Thank you Shadia

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Freesurfer December 2017