Freesurfer

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17 participants
30099 discussions

Parenchyma/CSF
by Mahmoud 20 Oct '14

20 Oct '14

Dear all, I used the the 3 steps of longitudinal analysis explained in freesurfer longitudinal tutorial and need to compute the ratio Parenchyma/CSF for each of time points. Is this equivalent to compute the (total gray matter volume + total cortical matter volume)/CSF from aseg.stats file ? Thank you, Mahmoud

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(no subject)
by Mahmoud 20 Oct '14

20 Oct '14

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Re: [Freesurfer] adding time points to longitudinal base template
by Martin Reuter 20 Oct '14

20 Oct '14

Hi Koushik, no, I cc the list, maybe someone has done tests or seen papers. I read somewhere on atlas construction, that 10 images are fine, but that is cross subject. Here we only have small changes within subject, so from my experience less are fine , BUT - 2 of course are not enough: in 2 the method is actually different (as the median in 2 is simply the average) . Starting with 3 a median intensity even exists for each voxel. - adding 1 new to 5 existing may work without sacrificing too much bias, but adding 10 to 5 is not a good idea. Also if the one that is added is very different from the first 5 (e.g. first 5 within a week, next 3 years later), then that will be problematic also. Best, Martin On 10/20/2014 12:07 PM, Govindarajan, Koushik Athreya wrote: > > Hi Martin, > > How are you? We had this below email conversation in March about > the longitudinal template and it's stability. You had mentioned that > with 5 time points, my template should be stable enough to patch > another timepoint. I have another study that has only 2 time points > and I was reading through your 2012 Longitudinal analysis paper that > had used 2 time points to compare with cross-sectional data. I was > wondering if you had any suggested literature for the number of time > points needed for stability of a template. > > Thanks > > Koushik Govindarajan > > *From:*Martin Reuter [mailto:mreuter@nmr.mgh.harvard.edu] > *Sent:* Friday, March 14, 2014 9:31 AM > *To:* Govindarajan, Koushik Athreya; freesurfer(a)nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] adding time points to longitudinal base > template > > Hi Koushik, > > there is a way to add time points without recreating the base: > recon-all -long <tpNsubjid> <longbasesubjid> -addtp -all > > This is what the recon-all help says about that: > "If a new timepoint needs to be added to a longitudinal run where a > base subject > has already been created (from prior timepoints), then the -addtp command > can be added to the -long command in order to 'fix-up' the longitudinal > stream to accept the new timepoint. Note that the base subject is *not* > recomputed using the new timepoint. This potentially introduces a > bias, and it > is recommended to NOT add a time point this way! Instead recreate the base > from all time points and run all longitudinals again." > > So it's up to you. But given you already have 5 time points in your > base and add only 1, you may be fine. The base should be pretty stable > with 5 and if the 6th is not too different, it should not matter much. > I don't think anyone has ever done a thorough analysis about adding > time points. > > Best, Martin > > On 03/11/2014 10:08 AM, Govindarajan, Koushik Athreya wrote: > > Dear FS experts, > > I have a serial study in which I have run > cross-sectional and longitudinal analysis on 5 time points. Now, I > want to add a 6^th time point to my dataset. Do I have to rerun my > base template creation step from scratch or is there a way to just > add further time points to an existing template? > > Thanks > > Koushik > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://urldefense.proofpoint.com/v1/url?u=https://mail.nmr.mgh.harvard.edu…> > > > > -- > Martin Reuter, Ph.D. > Assistant in Neuroscience - Massachusetts General Hospital > Instructor in Neurology - Harvard Medical School > MGH / HMS / MIT > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: > mreuter(a)nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> > reuter(a)mit.edu <mailto:reuter@mit.edu> > Web :http://reuter.mit.edu <https://urldefense.proofpoint.com/v1/url?u=http://reuter.mit.edu&k=yYSsEqip…> > > 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. > -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

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Bus error when trying to launch tksurfer
by Claire Morley 20 Oct '14

20 Oct '14

Good Morning, I have now been able to get the testing command: tksurfer bert rh pial to run, but it stops midway and issues a bus error. Please see the following script: DBM-Users-MacBook-Pro-4:~ dbmuser$ tksurfer bert rh pial subject is bert hemi is rh surface is pial surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/dbmuser checking for nofix files in 'pial' Reading image info (/Applications/freesurfer/subjects/bert) Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: vertices=133299, faces=266594 surfer: single buffered window surfer: tkoInitWindow(bert) Bus error Any idea what might be going wrong? I really need to use tksurfer to look at cortical thickness in gyrification in ROIs. (Oh and before I did this, I did set the environment as normal). Thanks so much for your help! Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot*

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pial vs. aseg
by Wegbreit, Ezra 17 Oct '14

17 Oct '14

Dear Freesurfer community, 1. Does the cortical segmentation (tinted red in the attached aseg_vs_pial.png) need to follow the pial surface (red line) precisely? Does the region under the cursor that is marked as cortex but is outside the pial surface count in the aparc results? In general, should I fix pial surfaces so that aseg and pial match precisely? For this participant, the skull strip and white matter segmentation both looked really good, especially in this region. 2. What about small pieces of remaining dura (or other outside brain material) labeled red as cortex in the aseg? Do they count in cortical thickness values, even though there's a clear gap between them and the cortex proper? (see cortex_outside_brain.png) I did find this old post on the mailing list but I was unsure if it answers my question: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg03807.html >From what I gather from this post and some others*, the aparc results are based on the surface and the aseg values are only relevant to subcortical structures, but I am still unsure if this is the correct interpretation. The original question in the mailing list concerns the hippocampus, but my questions are about the top of the cortex. Many thanks for answers! Ezra * e.g., http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg07810.html *___________________________________________________________* *Ezra Wegbreit, PhD* NIMH T32 Post-doctoral Research Fellow in Child Mental Health Pedi-MIND Program at Bradley Hospital Department of Psychiatry and Human Behavior Brown University Warren Alpert Medical School (401) 432-1615 ezra_wegbreit(a)brown.edu *___________________________________________________________*

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watershed error again
by Janosch Linkersdörfer 17 Oct '14

17 Oct '14

Hi all, I posted this problem earlier, but did not get an answer, so I am posting it again, sorry! --- recon-all runs smoothly for all my subjects but one. It throws the error "mri_watershed Error: indices out of bounds" and finishes (see https://www.dropbox.com/s/4del0uy8g1qw5az/recon-all.log ). The image quality does not seem to be different... The error has been discussed on the list ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021896.… ), but I don't know where in the brain and in which image space I should add control points or what else I can do to prevent this from happening. --- Thanks for your help, Janosch

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bbregister / mri_vol2vol with nifti file header
by Ajay Kurani 17 Oct '14

17 Oct '14

Dear Freesurfer users, I wanted to see if anyone knows what part of the file NIFIT header mri_vol2vol or mri_convert uses to write transform information from register.dat acquired from bbregister? I used the following commands to register the anatiomcal brain.mgz to the last time point of my EPI scan: bbregister --s ${sub}_FS --mov $bbrest_file --reg ${sub}_RS_register.dat --init-header --bold --frame $NP_last --nearest --template-out ${sub}.RS.template.nii mri_vol2vol --mov $loc_dir/spm/m${sub}.T1.nii --targ $SUBJECTS_DIR/${sub}_FS/mri/ brain.mgz --o $out_dir/brain_aligned.nii --inv --no-save-reg --reg $out_dir/${sub}_RS_register.dat When i view the images in Afni they look misaligned, but display perfectly in freesurfer (tkregister2 --mov EP_001.RS.template.nii --reg EP_001_RS_register.dat --surf) so I am assuming each program looks at a different field in the nifti file header. I used mri_vol2vol to apply the inverse transform of register.dat to brain.mgz so that it aligns with the EPI but for some reason it is not showing up correctly in afni so I wanted to get a better understanding of how freesurfer files write transformation information in nifti format (sform, qform, another part of the header) and if there is an easy way to get this into a format that afni reads correctly? Thanks, Ajay

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problem with gyrification index extraction
by elisa veronese 17 Oct '14

17 Oct '14

Dear FreeSurfers, I'm facing a problem with the estimation of local gyrification index. I've already performed the analysis with QDEC and the insertion of the MEASURE1 = pial_lgi line in the .Qdecrc file, but I'd like to see if it is possible to use the *aparcstats2table *command in order to have more concise and easy-to-read results. >From the QDEC GUI I've drawn a label in the temporal pole, and applied it to all my subjects (*mris_anatomical_stats -l rh.MR_TmpPole.label -t rh.pial_lgi -b -f s1/stats/rh.MR_TmpPole.stats s1 rh*) The problem is that when I call the *aparcstats2table --hemi rh --subjects s1 s2 ... --parc MR_TmpPole -t GI_MR_TmpPole.txt* I get a .txt file like this: rh.MR_TmpPole.area rh_rh.MR_TmpPole.label_area rh_WhiteSurfArea_area s1 6623.0 96171.8 s2 6257.0 85247.3 ... but I'm not sure what those numbers stand for. I'm afraid they have nothing to do with the gyrification index. Thank you, best elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology (RUBIN)* *Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http://icbn.uniud.it/tiki-index.php <http://icbn.uniud.it/tiki-index.php>*

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mkcontrast-sess errors no-octave
by elahe' yargholi 16 Oct '14

16 Oct '14

Dear Freesurfer experts, As I run mkcontrast-sess, I receive no octave error: fsl@fslvm6 MT_Localizer]$ mkcontrast-sess -analysis MT.lh -contrast MS -a 1 -c 2 INFO: Found 2 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 1.00000000000000000000 -1.00000000000000000000 mkcontrast -anadir MT.lh -wcond 1.00000000000000000000 -1.00000000000000000000 -sumconds -o MT.lh/MS.mat -wdelay 1 -no-octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile MT.lh/MS.mat nconds 2, wcond 1.00000000000000000000 -1.00000000000000000000 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR running mkcontrast mkcontrast -anadir MT.lh -wcond 1.00000000000000000000 -1.00000000000000000000 -sumconds -o MT.lh/MS.mat -wdelay 1 -no-octave Fri Oct 17 06:39:59 BST 2014 I have installed matlab and added path /home/fsl/Desktop/freesurfer/matlab /home/fsl/Desktop/freesurfer/fsfast/toolbox I will appreciate in advance if you possibly could help me to solve the problem. Best Regards, Elahe' Windows 7 and vmware10 Linux version: ------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/fsl/Desktop/freesurfer FSFAST_HOME /home/fsl/Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/fsl/Desktop/freesurfer/subjects MNI_DIR /home/fsl/Desktop/freesurfer/mni FSL_DIR /usr/local/fsl Current working directory: *pwd* */home/fsl* *which freesurfer* */home/fsl/Desktop/freesurfer/**bin/freesurfer* *which mkanalysis-sess* */home/fsl/Desktop/freesurfer/fsfast/bin/mkanalysis-sess* *which mkcontrast-sess* */home/fsl/Desktop/freesurfer/fsfast/bin/mkcontrast-sess* Command lines: *mkdir FIVA* *cd FIVA* *mkdir MT_Localizer* *cd MT_Localizer* *mkdir subj1sess1 * *cd subj1sess1* *unpacksdcmdir -src /home/fsl/Desktop/MTLocalizer/IMAGES -targ . -run 2 bold nii f.nii -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii -run 10 bold nii f.nii -run 11 bold nii f.nii* Within subj1sess1, made a text file named subjectname, and wrote subj001 (the name of my anatomical subject). *cd ..* *preproc-sess -s subj1sess1 -fsd bold -surface self lhrh -mni305 -fwhm 5 -per-run* For each run, a paradigm file (paradigm.par) is included. *mkanalysis-sess -a MT.lh -surface self lh -fsd bold -fwhm 5 -event-related -paradigm paradigm.par -nconditions 2 -refeventdur 16 -TR 2 -nskip 4 -polyfit 2 -spmhrf 0 -mcextreg* *mkanalysis-sess -a MT.rh -surface self rh -fsd bold -fwhm 5 -event-related -paradigm paradigm.par -nconditions 2 -refeventdur 16 -TR 2 -nskip 4 -polyfit 2 -spmhrf 0 -mcextreg * *mkcontrast-sess -analysis MT.lh -contrast M_S -a 2 -c 1 *

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FreeSurfer graphics requirement
by velocci＠physics.utexas.edu 16 Oct '14

16 Oct '14

Dear FreeSurfer users, I'm interested in using FreeSurfer on my Thinkpad X230 (Ivy Bridge) laptop with 8GB of RAM. My laptop does not have a dedicated graphics card, but rather an Intel HD Graphics 4000. Do you think I would still be able to run FreeSurfer, or should I really opt for a more capable machine? Thanks very much. I appreciate your time! Vince Velocci

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