Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30083 discussions

fcseed-sess ERROR: could not determine file for .../fmcpr
by Julio Alberto González Torre 19 Apr '16

19 Apr '16

Hi Freesurfer users. I am currently performing the steps of Functional Connectivity Walkthrough. And after resolving the problems in the first steps, specially in the preprocessing command (missing AFNI files), I'm now stuck in the 5th step: Creating the FC seeds for each subject. In the 4th step I've created the parameters for a region of interest. In this case, cheking the FreeSurferColorLUT.txt, I run this command to create the parameters for Left CA1 of Hippocampus (after the reconstruction, I performed the hippocampal subfields): fcseed-config -segid 552 -fcname L_CA1.dat -fsd rest -mean -cfg > mean.L_CA1.config In the 5th step, when I run the fcseed-sess command, I obtain this error and I'm unable to figure out why: fcseed-sess -s con_algon -cfg L_CA1.config ERROR: could not determine file for > /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr > stem2fname > /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr I've checked the "009" folder and there isn't any file with the name "fmcpr". Does someone have any idea how could I resolve this? Thanks!

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Re: [Freesurfer] PET voxelwise & Segmentation Fault during mri_glmfit-sim
by Elijah Mak 19 Apr '16

19 Apr '16

No, more like running the voxelwise comparisons only on voxels that have positive BP between 2 group. Is that possible? On another note, I am running into a puzzling "Segmentation fault" error with the following command: mri_glmfit-sim --glmdir lh_ad_hc.glmdir --cache 2 neg --cwp 0.05 --2spaces ================================================ Reading source surface /Users/MacPro/Documents/NIMROD_DTI//fsaverage/surf/lh.white Done reading source surface Reading annotation /Users/MacPro/Documents/NIMROD_DTI//fsaverage/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Segmentation fault ================================================ Strangely, I can't seem to reproduce this error consistently too. Sometimes, after a pause of few minutes, the exact same command works! This happens on smoothed and non-smooth PET data. I have attached the text outputs resulting from both scenarios 1) seg_fault and 2) no_seg_fault (about 10 minutes between each execution). The mri_glmfit-sim version is v .53.2.2 2015/08/28 19:00:13 I am running this on a Mac Pro with 64 GB RAM. Thanks again Best Wishes, Elijah

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mkanalysis-sess stimulusdelay parameter
by Joseph Dien 19 Apr '16

19 Apr '16

I’m taking a look at the effects of stimulus delay settings in one of my datasets so I was surprised to notice that the default setting of mkanalysis-sess is a delay of -TR/2 seconds. What is the reasoning for this? If, as I expect, it was just empirically found that it worked better than without, my question is whether this decision was made on the basis of all the event-related options or just some subset of them? I’m worried that this might be an optimization that isn’t appropriate for my particular parameter choices (FS 5.3, spmhrf0). Any comments would be appreciated. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park http://joedien.com

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CA2 hippocampal subfield in FS6.0
by Patrick Sezen 19 Apr '16

19 Apr '16

Dear FreeSurfers, I was running the FS 6.0 hippocampal subsegmentation and was wondering where the CA2 subfield disappeared to. Version 5.3 had a CA2-3 label, but in 6.0 I can only find CA3, is it implicated that CA2 is part of CA3 as well in 6.0? Sincerely, Patrick Sezen

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Re: [Freesurfer] preproc-sess error opening tmp brain_mask
by Mcnorgan, Christopher 19 Apr '16

19 Apr '16

du -h /tmp/ shows 256GB available, so that doesn’t seem to be it. Is the “not found” error telling me that a binary is not found, or that some expected output file is not found? I was looking for /bin/imtest and /bin/remove_ext, and those binaries indeed do not exist, but we’ve run Freesurfer on another dataset (but on another workstation, but neither were those two binaries to be found on that workstation). Is your /tmp space full? On 04/15/2016 12:54 PM, Mcnorgan, Christopher wrote: > > I was hoping the developers might be able to help with a problem I'm > having with a sub-step of preproc-sess. > I executed the following: > > preproc-sess -s FS_T1_501 -surface self lhrh -fwhm 6 -per-run -fsd bold > > In the relevant output, I see mktemplate-sess completed, followed by a > call to mkbrainmask-sess, which eventually reported: > > # ---------- Using FSL's BET to Extract Brain------------------ # > /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501/bold > bet.fsl /tmp/mkbrainmask_2623/in.nii /tmp/mkbrainmask_2623/brain -m -f 0.1 > /usr/local/freesurfer/bin/bet.fsl: 1: > /usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found > /usr/local/freesurfer/bin/bet.fsl: 1: > /usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found > /usr/local/freesurfer/bin/bet.fsl: 1: > /usr/local/freesurfer/bin/bet.fsl: /bin/imtest: not found > /usr/local/freesurfer/bin/bet.fsl: 153: [: =: unexpected operator > /usr/local/freesurfer/bin/bet.fsl: 231: > /usr/local/freesurfer/bin/bet.fsl: /bin/bet2: not found /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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(no subject)
by macara.p＠libero.it 19 Apr '16

19 Apr '16

Dear all, I need to compute the geodesic distance (i.,e. the distance on the cortical surface) between a series of vertices. Specifically, I want to compute the distance between all the vertices in the right hemisphere (>100000) and a series of vertices of interest (around 20000), always located in the right hemisphere. Ideally, my output should be a matrix right_verticesXvertices_of_interest where in each entry there is the geodesic distance between the pair of vertices. And I need to do this for hundreds of subjects! I tried to use mris_pmake: for i = right_vertices; for j=vertices_of_interest; command1 = ['/Applications/freesurfer_v5.3/bin/mris_pmake --subject 001 --hemi rh --surface0 white --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:' num2str(i) ',' 'endVertex:' num2str(j)] T(i)=evalc('system([command1])') end end But the problem is that it is way too much time consuming and it is difficult to store the results in a matrix. Is there a way to adapt this command for such high computations? I Are there other ways to obtain the geodesic distance between vertices, either than mris_pmake (for example a matlab function)? Thank you in advance,Marica

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how to add skull and scalp and how to convert RAS coordinates
by Chiara Bulgarelli 19 Apr '16

19 Apr '16

Dear FreeSurfer users, I am a PhD student from Birkbeck University and I am trying to segment some structural images of infants data. After the classical segmentation done with the ‘-recon all’ function, I am stuck with two issues: 1. How can I add the CSF, the skull and the scalp in my model? I know that with FS you can get just WM and GM. 2. How can I convert the RAS coordinates to MNI ones? I have been trying to look at these topics on line and on the FreeSurfer website, but I haven’t find anything useful so far. Many thanks in advance for your help! Best Regards Chiara ---------------- Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London cbulga01(a)mail.bbk.ac.uk // bulgarelli.chiara3(a)gmail.com

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Fwd: Exporting TIFF and rotating volume with tkmedit in Ubuntu 14.04
by Nasos Petridis 19 Apr '16

19 Apr '16

Hello, Recently, I started using freesurfer on a Ubuntu system. I've noticed two issues, when using tkmedit, for example: tkmedit subj_name norm.mgz -segmentation aparc.a2009s+aseg.mgz (i) When I try to save TIFF (Tools > Save TIFF), a TIFF file is created, and it can be opened in any image viewing program but is black. It's worth noting that when I try to save a cortical thickness surface view as tiff, using tksurfer tools, it works fine. (ii) When I try to rotate the volume (Tools > Volume > Rotate Volume), I cannot enter an angle in the "Degrees" dialogue box, ie I type the number but no number appears neither doe the cursor move. I've tried both freesurfer 5.3 Linux distributions (centos4, centos6) with no difference. I'm running Ubuntu 14.04LTS. Do I need to install any packages in Ubuntu? Any suggestion how to tackle those two issues would be greatly appreciated. Many thanks, Nasos

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Export Freesurfer labels to SPM ROIs
by Mohamed Abdelhack 19 Apr '16

19 Apr '16

Hello FS community, I have made some custom labels based on retinotopy data and I wish to export these as SPM ROIs so that I can use some specific tools. I grouped the labels into an annotation file and I used mri_label2vol to convert it into nifti, I then imported it into matlab and I get a volume with each pixels corresponding to a number. How can I confirm if the coordinates that I have used to export these labels are aligned well with the data in SPM coordinate system? Thank you, Mohamed,

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How to find the information from MRI data file
by Muhammad Naveed Iqbal Qureshi 18 Apr '16

18 Apr '16

Hi, How can I find the following information from the MRI volume data already preprocessed with Freesurfer. 1. Echo time 2. Repetition time 3. Flip angle Thank you. Best Regards, Muhammad Naveed Iqbal Qureshi P please don't print this e-mail unless you really need to

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