Freesurfer December 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
175 discussions

volume and mean intensity values from single nii file with multiple ROIs
by Anik Dar 06 Dec '18

06 Dec '18

External Email - Use Caution Dear All, I have segmented the midbrain of each subjects into different subregions (peduncle, substantia nigra, red nucleus etc) using an atlas. I am trying to extract the volume of each region (the regions are labeled 101, 102, 103 etc) and also trying to extract the mean intensity from MPRAGE from each of these regions. Is there a way to do this in freesurfer tools ? I realize that there is no color lut / index file associated with this atlas in freesurfer. Please let me know. Thank you, Ani

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fsaverage6 FS6
by Sanfelici, Rachele 06 Dec '18

06 Dec '18

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hippocampus cortex surface
by Yixin Ma 06 Dec '18

06 Dec '18

External Email - Use Caution Hi Freesurfer experts, After running the segmentation of hippocampus subfields, I'm wondering if I can get the surface of the gray matter and white matter of hippocampus in addition to subfields. My goal is to divide the hippocampus cortex into multiple layers. Thanks for your help in advance. Yixin

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Necessity of Matlab for Using FsFast
by Maedeh Khalilian 06 Dec '18

06 Dec '18

External Email - Use Caution Dear experts, Is it necessary to install Matlab to use FsFast for functional connectivity? Thanks in advance Best Maedeh,

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problem with mri_label2vol
by Mareike Grotheer 06 Dec '18

06 Dec '18

External Email - Use Caution Hello FreeSurfer Developers, I am trying to bring functional ROIs defined in a different program into FreeSurfer, so that I can dilate them into the white matter with –proj abs, but I am running into a problem I was hoping you could help me with. Here are the steps I am taking: 1)I am converting my ROIs, which are in nifti format, to FreeSurfer labels using: cmd = ['mri_vol2label --c ' outFile{1} ' --id ' num2str(roiVal(roi)) ' --l ' saveLabel{1} ' --surf ' subject ' ' hemi ]; unix(cmd); 2)Next, I want to dilate the labels using this: cmd = sprintf('!mri_label2vol --subject %s --label %s --o %s.nii.gz --hemi %s --reg %s.dat --temp %s --proj abs -7 0 .1 --fillthresh .001', fs_subject,labelFileName,niftiRoiName,hemisphere, tmpRegFile, regMgzFile); eval(cmd); This does not work, I get the following Error Message: ERROR: label my_label.label is not a surface label. I can circumvent this error by manually opening the label in tksurfer and saving it again. After that mri_label2vol runs without error. I assume that tksurfer automatically converts the label to a surface label. While this solves my problem in principle, I have many labels and am hoping that there may be a better way. Do you have any ideas how one could do this automatically? I am running the above code in Matlab R2015a. I am using FreeSurfer version 6.0.0 on Ubuntu 12.04 LTS. Thank you very much, Mareike

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Registering Anatomical Parcellation to DWI
by Maedeh Khalilian 06 Dec '18

06 Dec '18

External Email - Use Caution Dear FreeSurfer experts, I have a parcellation and a whole brain white matter files which are the outputs of FreeSurfer. I want to register them to my DWI. I mean I want my parcellation and white matter to be in the physical space of my DWI. Can FreeSurfer do it for me? If not , can you suggest me a toolbox that can do it fast? I would be grateful if u could help me. Cheers, Maedeh,

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Fwd: fcseedcor output
by Sara Jafakesh 06 Dec '18

06 Dec '18

External Email - Use Caution Dear freesurfer experts, I want to calculate corrolation between two seeds with freesurfer-linux-centos6_x86_64_stable_pub-v6 .after using fcseed-config and fseed-sess , I used fcseedcor. the command that I trying to run is as follow: fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat but the output of fcseedcor is not .dat file ( the connectivity matrix for my result 2*2 matrix) as it has been explained in the fcssedcor help. the output is just the .log file named seedcor2.dat.log. although it has been done without error. I really dont know what is the problem. I would be grateful if you could help me. best regards, sara

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Direction of significant group comparison
by Backhausen, Lea 06 Dec '18

06 Dec '18

External Email - Use Caution Dear FreeSurfer experts, I am running whole-brain based group comparisons of cortical measures between a patient group and a control group using glm-fit and Monte-Carlo correction for multiple comparisons. It works fine but I am not sure where to find information on which group has more or less volume, for example, in a significant cluster. I use the xxx.sig.cluster.summary files which give me something like this: ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 3.806 82573 3279.56 44.3 22.8 29.5 0.00020 0.00000 0.00040 5510 11256.20 rostralmiddlefrontal 2 2.099 122283 806.53 38.4 -69.6 44.6 0.68055 0.67327 0.68774 1654 2759.09 inferiorparietal Is the direction hidden somewhere or in another file? Do I have to run additional commands to get to the information? Thank you so much for any advice! Best Lea ------------------------------ Lea Backhausen Research Assistant Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden.de/>

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Re: [Freesurfer] mris_preproc paired diff outputs 0 values
by Sims, Sara A 06 Dec '18

06 Dec '18

External Email - Use Caution I have now gotten this to run on 3 subjects. However I have 786 subjects and need to find the bad apple. Is there a way I can do quality checks on each subject’s difference map in fsaverage space that mris_preproc has made? Basically I want to cycle through the concatenated file in a systematic way that hopefully doesn’t involve me opening them one at a time in freeview. How could I do this? Sara Sims From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Sara Sims <snolin(a)uab.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, December 3, 2018 at 10:56 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] mris_preproc paired diff outputs 0 values External Email - Use Caution Hello, I am trying to do a paired difference analysis of two runs of probtrackx (I have already put them on the surface). The two conditions are “central” and “far” for each subject. I have already checked the individual subjects data and it does indeed have values. Here is a sample of my subject list: 100206.central 100206.far 100307.central 100307.far 100408.central 100408.far …etc. Here is my mris_preproc script: mris_preproc --target fsaverage --hemi lh --isp $in/FP/100206.central/lhsurf.mgh --isp $in/FP/100206.far/lhsurf.mgh --isp $in/FP/100307.central/lhsurf.mgh --isp $in/FP/100307.far/lhsurf.mgh --isp $in/FP/100408.central/lhsurf.mgh --isp $in/FP/100408.far/lhsurf.mgh … --out $out/preproc_FP_cf_lh/lh.paired-diff.FP_cf.mgh --f $sublist --paired-diff The output log shows no errors, the number of inputs equals the number in the subject list and it creates a file but it’s all zeros. I just have no idea as to why this would happen? Thanks, Sara Sims

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visual cortex {Disarmed}
by 郑凤莲 06 Dec '18

06 Dec '18

External Email - Use Caution Hi experts, I want to do some research on the cortical thickness of visual cortex using FS 6.0. Is there specified or associated cortex model for the segmentation of visual cortex? Thanks for your reply in advance. I need your help. Sincerely, Zheng | | 郑凤莲 | | 邮箱：zhengfenglian0105(a)163.com | 签名由网易邮箱大师定制

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Freesurfer December 2018