Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

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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Research Assistant and Psychologist Positions at Max Planck Institute-CBS, Leipzig, Germany
by Katharina von Kriegstein 18 Apr '16

18 Apr '16

Applications are welcomed for two positions in the Human Communication group lead by Katharina von Kriegstein at the Max Planck Institute for Human Cognitive and Brain Sciences (MPI-CBS) in Leipzig, Germany. Research in the group focuses on the investigation of neural mechanisms of human communication using a broad spectrum of neuroscientific methods (functional and structural MRI, MEG, tDCS, TMS). Research involves typically developed populations as well as populations with developmental communication deficits (developmental dyslexia, autism spectrum disorder, phonagnosia, proposagnosia). Research Assistant: http://www.mpg.de/10451891/research-assistant-lab-manager The position will involve recruiting participants, running behavioural tests, assistance with data-acquisition in MRI, TMS and tDCS studies, assistance with data analyses, grant writing and literature searches, attending lab meetings, supervising undergraduate students in the lab and overseeing day-to-day lab operations. The position is available part or full time. It includes the opportunity to pursue a variety of research opportunities that can result in authorship on academic publications. Psychologist: http://www.mpg.de/10451838/20161504-1 (in German) The position is available part time. The main duty will be to support diagnostic testing in people with communication disorders (e.g. autism spectrum disorder, dyslexia, developmental prosopagnosia). The position offers the possibility to be involved in research. For further information on the positions and instructions on how to apply please follow the links provided above. --- Katharina von Kriegstein Max Planck Research Group Leader Max Planck Institute for Human Cognitive and Brain Sciences Stephanstr. 1A, 04103 Leipzig, Germany Professor of Cognitive and Clinical Neuroscience Humboldt University of Berlin Rudower Chaussee 18, 12489 Berlin, Germany Phone +49 (0) 341-9940-2476 Fax +49 (0) 341-9940-2448 http://www.cbs.mpg.de/independent-research-groups/human-communication

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Freesurfer 6.0 Hippocampal Subfield Analysis
by Ajay Kurani 16 Apr '16

16 Apr '16

Hello Freesurfer Experts, I am having a bit of trouble with the hippocampal subfield analysis using the Freesurfer 6.0 program. My data is organized as /AnalysisFolder/Group/Subject/Anatomical/SUB_FS .. where SUBJECTS_DIR=/AnalysisFolder/Group/Subject/Anatomical/ and my subject specific folder is SUB_FS. Not all data is located in /Anatomical but rather in /Group for each group. I ran the following based on https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation: recon-all -s ${sub}_FS -openmp 4 -itkthreads 4 -hippocampal-subfields-T1 cd $SUBJECTS_DIR/${sub}_FS/mri/ kvlQuantifyHippocampalSubfieldSegmentations.sh This created 6 files: lh.hippoSfLabels-T1.v10.1mm.mgz lh.hippoSfLabvels-T1.v10.mgz lh.hippoSfVolumes-T1.v10.txt rh.hippoSfLabels-T1.v10.1mm.mgz rh.hippoSfLabvels-T1.v10.mgz rh.hippoSfVolumes-T1.v10.txt I received the following output error in the terminal even though files were generated: kvlQuantifyPosteriorProbabilityImages /usr/local/bin/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt terminate called after throwing an instance of 'itk::ExceptionObject' what(): itkMGHImageIO.cxx:217: itk::ERROR: MGHImageIO(0xe1a620): Can't find/open file: posterior_Left-Hippocampus.mgz /usr/local/bin/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: 2000993 Aborted (core dumped) kvlQuantifyPosteriorProbabilityImages /usr/local/bin/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt failed to do kvlQuantifyPosteriorProbabilityImages /usr/local/bin/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt When I open lh.hippoSfVolumes I see the following: Hippocampal_tail 403.806174 subiculum 309.796102 CA1 384.206539 hippocampal-fissure 143.951401 presubiculum 226.899518 parasubiculum 49.511870 molecular_layer_HP 381.834418 GC-ML-DG 196.542924 CA3 155.112708 CA4 181.563384 fimbria 31.116787 HATA 26.871413 Whole_hippocampus 2347.261836 I also found a second set of instructions for quantifying Hippocampal subfields: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields This page says to use : quantifyHippocampalSubfields.sh <T1>-<analysisID> <output_file> <OPTIONAL_subject_directory> so I ran: SUBJECTS_DIR=/AnalysisFolder/Group/Subject/Anatomical/ cd $SUBJECTS_DIR/${sub}_FS/mri/ quantifyHippocampalSubfields.sh T1-${sub}_FS test.txt $SUBJECTS_DIR/${sub}_FS/mri No file was generated for this subject in $SUBJECTS_DIR/${sub}_FS/mri (1)My question for kvlQuandify is if posterior_Left-Hippocampus.mgz is supposed to be created or if this is a file that was generated from a previous version of the program that is supposed to be removed from kvlQuantifyHippocampalSubfieldSegmentations.sh for Freesurfer v6.0 dev? If it is supposed to be created, I do not see this file in /mri for any subjects I tested this script on. (2) Can I use kvlQuantifyHippocampalSubfieldSegmentations or quantifyHippocampalSubfields to calculate each individual subject's volumes for each segment generated in Freeserfer 6.0? Which is the correct program to use? The reason for not using the whole group of subjects with one of these tools is that I want to use SPSS to correlate each subfield volume with at variety of clinical measures, however I may be using these tools incorrectly and there may be a better way to do this. Thanks, Ajay

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Re: [Freesurfer] PET voxelwise
by Elijah Mak 15 Apr '16

15 Apr '16

Dear Doug, One more question: There are many voxels with negative binding potentials in this dataset, mostly in the CSF/ventricular regions. Can I restrict the mri_glmfit to focus only on the voxels with positive BP? Best Wishes, Elijah

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preproc-sess error opening tmp brain_mask
by Mcnorgan, Christopher 15 Apr '16

15 Apr '16

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 mri_binarize --i /tmp/mkbrainmask_2623/brain_mask.nii --min .01 --o /tmp/mkbrainmask_2623/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_2623/brain_mask $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501/bold cmdline mri_binarize --i /tmp/mkbrainmask_3238/brain_mask.nii --min .01 --o /tmp/mkbrainmask_3238/brain_mask.nii sysname Linux hostname wernickesarea machine x86_64 user chris input /tmp/mkbrainmask_3238/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_3238/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0 It's not obvious from the tail end of the output that this didn't work out, but this process finished in just a couple of seconds (making it unlikely that any smoothing or slice time correction was performed), and there was no brain_mask.nii file to be found either in /tmp/ or in the session folder. Those "not found" errors seem relevant, but I can't imagine what to do about them.

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mri_vol2surf after recon-all
by Trisanna Sprung-Much 15 Apr '16

15 Apr '16

Hi Freesurfer I have some labels (.mnc) that are painted voxels generated from a Montreal Neurological Institute software. I am trying to project the labels onto the surfaces generated from recon-all that I applied to the corresponding MRI volumes. *I used mri_vol2surf: * mri_vol2surf --src labels.mnc --out test.mgz --srcreg talairach.auto.xfm --hemi lh *and got the following error:* Error reading inplaneres from talairach.auto.xfm Do I need a .dat file? If so, how can I attain it? Essentially, what is the registration file that I am supposed to be using? Many thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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correcting mri_glmfit results
by Clara Kühn 15 Apr '16

15 Apr '16

Dear FreeSurfer experts, I'm trying to run a mri_glmfit on my first time point (out of 3). I ran the glm with this: mri_glmfit --table $SUBJECTS_DIR/aparcs_stats_sc1.txt --fsgd $SUBJECTS_DIRfsgd_sc1.txt --C $SUBJECTS_DIR/group.mtx --surf 87kids_template lh --cortex --glmdir $SUBJECTS_DIR/glm/lh.thick_group.glmdir So far so good :) Now when I try to apply the Monte Carlo correction with this: mri_glmfit-sim --glmdir $SUBJECTS_DIR/qdec/87kids/glm/lh.thick_group.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor --cache 3.0 neg --cwp 0.05 --2spaces I get the error "fwhm: Undefined variable." So I tried to run the glmfit with the --y flag and use the lh.thickness_sm10.mgh file but I created that when registering and smoothing ALL my time points to the template, so I get this error: "ERROR: dimension mismatch between y and X. y has 224 inputs, X has 72 rows." I have looked at mri_glmfit-sim --help but there seems to be no flag for fwhm only an overwriting one. Should I register and smooth the data again for the separate time points or is there another way to deal with that? What could I do to correct my glm data? Cheers, Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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Simple algorithm question
by Gamaliel Huerta Urrea 15 Apr '16

15 Apr '16

Hi all I would like to be certain about what are the algorithms that Freesurfer use for Segmentation of surfaces (brain-skull-skin), and after, what is the algorithm for surfaces construction and tessellation?. And moreover i would like to know if you have some papers about this topic. Cheers. -- *Gamaliel Huerta* *Ingeniero Civil Biomédico* *HealthCare Analytics* *Centro Interdisciplinario de Innovación en Salud* *Universidad de Valparaíso*

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Re: [Freesurfer] PET voxelwise
by Elijah Mak 15 Apr '16

15 Apr '16

Hi Doug, I edited the registration by hand (after bbregister) in Freeview, saving the PET_2_T1 volume. In Freeview (dev FS6) : Tools -> Transform Volume --> Tweaked rotation and translation --> Save Volume As --> Clicked "Do not resample voxel data when saving (only update header)" Using this method, I realise I could simply specify -regheader without feeding the .lta for mri_vol2surf and it seems to work well. Best Wishes, Elijah How did you edit the registration? Does it work with the unedited version? On 04/13/2016 10:21 AM, Elijah Mak wrote: > Hi Doug, > > One more question about feeding the -reg to mri_vol2surf, please. > > I am specifying the registration .lta because I have made edits to it, > > mri_vol2surf --src FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz > --out FS6_24551_MPRAGE_Neuro.nii/surf/lh.PETSurfce.mgh --projfrac 0.5 > --hemi lh --reg FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz.lta > --trgsubject fsaverage > > I get the following error: > > srcvol = FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz > > srcreg = FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz.lta > > srcregold = 0 > > srcwarp unspecified > > surf = white > > hemi = lh > > trgsubject = fsaverage > > surfreg = sphere.reg > > ProjFrac = 0.5 > > thickness = thickness > > reshape = 0 > > interp = nearest > > float2int = round > > GetProjMax = 0 > > INFO: float2int code = 0 > > Done loading volume > > Input reg is LTA > > > > type = 0 # LINEAR_VOX_TO_VOX > > nxforms = 1 > > mean = 0.0000 0.0000 0.0000 > > sigma = 1.0000 > > 1 4 4 > > 9.996573328971863e-01 -2.963314531370997e-03 2.600867860019207e-02 > -2.005096435546875e+00 > > 1.517883041479706e-18 9.935718178749084e-01 1.132032126188278e-01 > -2.398274230957031e+01 > > -2.617694810032845e-02 -1.131644248962402e-01 9.932314157485962e-01 > 1.568508148193359e+01 > > 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 > 1.000000000000000e+00 > > src volume info > > valid = 1 # volume info valid > > filename = > /Users/MacPro/Documents/NIMROD_DTI/FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz > > volume = 256 256 256 > > voxelsize = 1.000000000000000e+00 1.000000000000000e+00 > 1.000000000000000e+00 > > xras = -1.000000000000000e+00 -2.328306436538696e-10 > 0.000000000000000e+00 > > yras = -1.862645149230957e-09 -2.991509973071516e-08 > -1.000000000000000e+00 > > zras = 0.000000000000000e+00 1.000000000000000e+00 1.091393642127514e-10 > > cras = 1.471549987792969e+00 -1.038517761230469e+01 > 1.970146179199219e+01 > > dst volume info > > valid = 1 # volume info valid > > filename = > /Users/MacPro/Documents/NIMROD_DTI/FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz > > volume = 256 256 256 > > voxelsize = 1.000000000000000e+00 1.000000000000000e+00 > 1.000000000000000e+00 > > xras = -1.000000000000000e+00 -2.328306436538696e-10 > 0.000000000000000e+00 > > yras = -1.862645149230957e-09 -2.991509973071516e-08 > -1.000000000000000e+00 > > zras = 0.000000000000000e+00 1.000000000000000e+00 1.091393642127514e-10 > > cras = 1.471549987792969e+00 -1.038517761230469e+01 > 1.970146179199219e+01 > > fscale 0.150000 > > ERROR: source volume is neither source nor target of the registration > > This error does not appear when I use --regheader though? > > Best Wishes, > > Elijah > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Centergr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/… Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 athttp://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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geodesic distance between vertices
by macara.p＠libero.it 15 Apr '16

15 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])') endend 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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