Freesurfer March 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
247 discussions

Problem about the fMRI Analysis of correlation？
by Linda Xu 28 Mar '14

28 Mar '14

Dear Sir, My experiment design is let the two group of subjects watch a movie and calculate the correlation between two condition. Now I get the correlation result from AFNI. I want to calculate the correlation different between the two group by using freesurfer. However the group analysis in freesurfer need the paradigm file to get the constrast file for matlab. But I do not know how can a stimulate as movie can be serve as? I do not know how to write the paradigm at this time. My question is: My stimulate is a 10 minute movie. How can I get the correlation different of two group by using freesurfer? Could you give me some advice?

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Re: [Freesurfer] Problem about the fMRI Analysis?
by Linda Xu 28 Mar '14

28 Mar '14

Dear Douglas, What should I do next? I do not know how to use the freesurfer to calculate the correlation different of two group. So could you give me some advice? Yours Linda 2014-03-27 19:18 GMT-04:00 Linda Xu <lynda.bme(a)gmail.com>: > Dear Douglas, > OK, I will figure it out. And my next question is that, What should I do > next? I do not know how to use the freesurfer to calculate the correlation > different of two group. So could you give me some advice? > > > 2014-03-27 19:06 GMT-04:00 Douglas Greve <greve(a)nmr.mgh.harvard.edu>: > > >> Surface-based analysis is an alternative to talairach-based analysis. It >> does not make sense to do both. Is the AFNI talairach space affine (ie, 12 >> dof)? If so, then it is possible to undo the resampling to talairach space. >> You will need to know which space the afni results are in (ie, MNI152 or >> MNI305 or something else? 1mm or 2mm?) >> doug >> >> >> >> >> >> On 3/27/14 5:06 PM, Linda Xu wrote: >> >> Dear Douglas, >> I do not understand what's your meaning? Yes I think the afni results has >> already alined to T1.mgz, so it is already in talairach space. I do not >> know what to do next? As I have two groups subjects. I do not know what to >> analysis the correlation different between two groups by using >> surface-based analysis of freesurfer. >> Linda >> Message: 5 >> Date: Wed, 26 Mar 2014 14:05:46 -0400 >> From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Problem about the fMRI Analysis? >> To: freesurfer(a)nmr.mgh.harvard.edu >> Message-ID: <533316FA.50903(a)nmr.mgh.harvard.edu> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> >> Are the AFNI results already in talairach space? If so, then there is no >> point in going to surface space. >> doug >> >> >> On 03/26/2014 01:22 PM, Linda Xu wrote: >> > I get the correlation result between two condition of the functional >> > data by using AFNI( I do not know how to do correlation by using >> > freesurfer) >> > And then I use the bbregister to aline the correlation result (produce >> > by Afni) to the anatomical result produced by using freesurfer. >> > Next I using mri_vol2surf to aline the each one's functional result to >> > the fsaverage offer by freesurfer. >> > My question is :1 Should I need to do mri_vol2vol next for each subject? >> > 2 I have two group of subjects. I want to know >> > if there is some correlation different between them? What should I do >> > next? >> > Thanks very much! >> > Linda >> > >> >> >> The information in this e-mail is intended only for the person to whom >> it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > >

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how to capture blurred GM/WM junction?
by Markus Gschwind 28 Mar '14

28 Mar '14

Dear all, I would like to capture regions where the gray matter/ white matter junction is blurred in order to detect possible focal cortical dysplasias. As I understood the WM/GM segmentation is done by the script mri_segment. Would it be possible detect those regions where the gradient between GM and WM regions is low? I imagined that running mri_segment several times, with each time a different lower GM threshold and higher WM threshold, and then calculating the diference between the results, might give such information. I am very much interested in what you think about this approach and how to do it practically. For info here are the optional flags of mri_segment: -slope <s> set the curvature slope (both n and p) -pslope <p> set the curvature pslope (default=1.0) -nslope <n> set the curvature nslope (default=1.0) -debug_voxel <x y z> set voxel for debugging -auto automatically detect class statistics (default) -noauto don't automatically detect class statistics -log log to ./segment.dat -keep keep wm edits. maintains all values of 0 and 255 -ghi, -gray_hi <h> set the gray matter high limit (default=100.000) -wlo, -wm_low <l> set the white matter low limit (default=90.000) -whi, -wm_hi <h> set the white matter high limit (default=125.000) -nseg <n> thicken the n largest thin strands (default=20) -thicken toggle thickening step (default=ON) -fillbg toggle filling of the basal ganglia (default=OFF) -fillv toggle filling of the ventricles (default=OFF) -b <s> set blur sigma (default=0.25) -n <i> set # iterations of border classification (default=1) -t <t> set limit to thin strands in mm (default=4) -v verbose -p <p> set % threshold (default=0.80) -x <filename> extract options from filename -w <w> set wsize (default=11) -u usage Thank you very much for all comments! Markus

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freesurfer install
by limengsecret 28 Mar '14

28 Mar '14

Hi freesurfer， I ?installed the package of freesurfer according to the intruction of freesurfer website. But when I checked whether it was installed successfully, I inputed?the commands following: 1)?tksurfer bert rh pial? Couldn't create output file .xdebug_tksurfersubject is bert hemi is rh surface is pial surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/bin surfer: can't create file surfer.log in cwd surfer: surfer.log created in /tmp surfer: session root data dir ($session) reset to: surfer: /tmp Reading image info (/usr/local/freesurfer/subjects/bert) Reading /usr/local/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/orig.mgz 2) tkmedit bert orig.mgz?Couldn't create output file .xdebug_tkmedit =================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu : : Now exiting... : 3) ?qdec?qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory yxk-ThinkStation-D30:/usr/local/freesurfer/bin> ? Thus, I want to know the reason why these problems occurred, and the solution to these problems. Thank you very much Meng

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Extracting ROI information using created label
by Clint Johns 28 Mar '14

28 Mar '14

Hi, We are having some trouble extracting ROI (thickness) information using a label we created. After conducting a group analysis, we drew an ROI label based on the results. We used tksurfer to draw the label (we couldn't do this in freeview, which would freeze for some reason). However, at this point we're kind of stuck. The tutorial slides give the way to extract ROI information using existing labels, and then how to create a label, but not how to use the custom label to extract the relevant information. Any advice would be appreciated! Thanks, Clint -- I remain... Clinton L. Johns, Ph.D. Research Scientist, Haskins Laboratories 300 George Street New Haven CT 06511 speech: 203-865-6163 x240 fax: 203-865-8963 net: johns(a)haskins.yale.edu

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error
by xiangbo_2010 28 Mar '14

28 Mar '14

Dear experts, when I run the "qdec", and the wrong information appear in following: qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory I hope some experts to help me ,thank you very much! -- Bo Xiang State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China The Mental Health Center and the Psychiatric Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China Phone: +8615281056345 QQ: 529111494 Skype: xiang.bo3 向波四川大学华西医院生物治疗国家重点实验室，华西医院精神医学研究室成都市武侯区人民南路三段中四川大学华西校区，610041 E-mail: xiangbo_2010(a)126.com / xiangboyulan2012(a)gmail.com 电话：15281056345 QQ：529111494 Skype：xiang.bo3

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mc-bbr
by SHAHIN NASR 27 Mar '14

27 Mar '14

Hi, For a project in which subjects have repeated head movements, I want to register every TR to anatomical scans separately to reduce the effect of head movement as much as possible. When I checked the old posts, I noticed that there has been a code since 2011 ( https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-December/021691.…) to do this (named mc-bbr). But I am not sure if it is valid any more and not sure how does it works. As far as I see, there is no flag for mc-bbr or something similar to that in preproc-sess. I appreciate if you guide me through it. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Re: [Freesurfer] Problem about the fMRI Analysis?
by Linda Xu 27 Mar '14

27 Mar '14

Dear Douglas, I do not understand what's your meaning? Yes I think the afni results has already alined to T1.mgz, so it is already in talairach space. I do not know what to do next? As I have two groups subjects. I do not know what to analysis the correlation different between two groups by using surface-based analysis of freesurfer. Linda Message: 5 Date: Wed, 26 Mar 2014 14:05:46 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Problem about the fMRI Analysis? To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <533316FA.50903(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Are the AFNI results already in talairach space? If so, then there is no point in going to surface space. doug On 03/26/2014 01:22 PM, Linda Xu wrote: > I get the correlation result between two condition of the functional > data by using AFNI( I do not know how to do correlation by using > freesurfer) > And then I use the bbregister to aline the correlation result (produce > by Afni) to the anatomical result produced by using freesurfer. > Next I using mri_vol2surf to aline the each one's functional result to > the fsaverage offer by freesurfer. > My question is :1 Should I need to do mri_vol2vol next for each subject? > 2 I have two group of subjects. I want to know > if there is some correlation different between them? What should I do > next? > Thanks very much! > Linda >

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space conversion in the mri_surf2vol
by charujing123 27 Mar '14

27 Mar '14

Dear FS experts, I completed mri_surf2vol converting lh.gender_age.thickness.10.mgh into test.nii based on the fsaverage template. I want to know what space for the two files(*.mgh and *.nii) respectively? Thanks. All the best. Rujing Zha 2014-03-27 charujing123

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MNI CONVERSION PROBLEM
by Gabriel Gonzalez Escamilla 27 Mar '14

27 Mar '14

Dear FS experts, I've been dealing with the conversion to MNI152 of some volumetric labels of my subjects extracted with mris_extract_label in FS v.5.1 but, I've been unable to succeed. I've tried bbregister and mni152reg commands, both of them give me an example to check at the registrations using tktegister2, when I use it everything seems to be OK, but when I do apply with mri_vol2vol any of the matrices to the volumetric masks, they appear to be rotated, I don't know how is it possible or how to fix it. Any help will be really appreciated. Many thanks in advanced, Gabriel

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Freesurfer March 2014