Re: [Freesurfer] Fix topology correcting defect

External Email - Use Caution I would like to follow-up this thread. I've encountered similar problem about the recon-all process is stuck at fix topology for a long time (10+ hours) [Centos 6, Freesurfer 6.0.0] I can't see any problem from log files, just as follows 1. #@# Fix Top

[Freesurfer] Difference between target surface and target of registration file in mri_surf2surf

External Email - Use Caution Hello, I am trying to understand some code I came across and am having trouble understanding the difference between the target surface in mri_surf2surf and the surface used as target for the registration. The code first uses freesurfer_registerXhem reg

Re: [Freesurfer] surface cortical lesions mask --> annotation file ???

Yes, if you only have one label. You will probably want to change the name to Lesion or somthing. You can also change the color by changing the RGB On 2/15/19 2:01 PM, Barletta, Valeria wrote: Ok I did and inserted only this: #No. Label Name:R G B A 1 Left-Ce

Re: [Freesurfer] surface cortical lesions mask --> annotation file ???

Ok I did and inserted only this: #No. Label Name:R G B A 1 Left-Cerebral-Exterior 70 130 180 0 since I binarized the lesion masks and when creating the label I assigned value 1 (with the option --id 1). Is it correct? Thanks, Vale __

Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc

Do you mean that it continues to run but does not do anything (eg, print more to the terminal) or that it has crashed? If it is hanging, how long? Nothing looks suspicious in the output. On 2/15/19 12:59 PM, ?? wrote: External Email - Use Caution Hi Greve, i solved this problem, but ha

[Freesurfer] Group level T map

External Email - Use Caution Dear freesurfers, I am trying to find a t-map for my group level test. In a one sample group mean test folder I have: gamma.nii.gz gammavar.nii.gz cnr.nii.gz sig.nii.gz F.nii.gz The gamma.nii.gz corresponds to the beta.nii.gz from the folder above,

Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc

External Email - Use Caution For more than 3 hours ---Original--- From: "Greve, Douglas N.,Ph.D." Date: Fri, Feb 15, 2019 20:03 PM To: "freesurfer@nmr.mgh.harvard.edu"; Subject: Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc how long? On 2/15/19 2:49 PM, ?? wrote

Re: [Freesurfer] zero values when run recon-all with T2pial flag (V6.0)

External Email - Use Caution Thanks for taking a look at the file I sent! I think I have figured out the issue for the most part. While it shows that there is data in the recon-all log for the various cortical regions and eTIV, the data I extracted using aparcstats2table gives me z

Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc

how long? On 2/15/19 2:49 PM, ?? wrote: External Email - Use Caution Hi Thanks for your quickly reply, yes continue to run but not print more on terminal anymore. ---Original--- From: "Greve, Douglas N.,Ph.D." Date: Fri, Feb 15, 2019 19:01 PM To: "frees

Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc

External Email - Use Caution Hi Thanks for your quickly reply, yes continue to run but not print more on terminal anymore. ---Original--- From: "Greve, Douglas N.,Ph.D." Date: Fri, Feb 15, 2019 19:01 PM To: "freesurfer@nmr.mgh.harvard.edu"; Subject: Re: [Freesurfer] lh.PDDvsH

Re: [Freesurfer] surface cortical lesions mask --> annotation file ???

you have to create your own. Use FreeSurferColorsLUT.txt as your template On 2/15/19 1:08 PM, Barletta, Valeria wrote: Ok thank you, it works but there is a problem... The command mris_label2annot requires a ColorTable file. As I tried to use FreeSurferColorLUT.txtI got a list of all region

Re: [Freesurfer] dt_recon error MatrixReadTxT: could not scan value [1][1]

External Email - Use Caution Thanks! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com * 443-254-6298 On Fri, Feb 15, 2019 at 11:18 AM Greve, Douglas N.,Ph.D. < dgr...@mgh.harva

Re: [Freesurfer] surface cortical lesions mask --> annotation file ???

Ok thank you, it works but there is a problem... The command mris_label2annot requires a ColorTable file. As I tried to use FreeSurferColorLUT.txtI got a list of all regions I did not need. What kind a ColorTable file shall I provide to create an annotation file for cortical lesions only?

[Freesurfer] Templates used for eTIV computation in recon-all

External Email - Use Caution Dear experts, We were comparing recon-all output of Freesurfer 5.3 and 6.0 in our database, and found that eTIV values can increase by up to 40% going from 5.3 to 6.0. However, closer inspection revealed that it was not due to the version per se, but h

Re: [Freesurfer] Unexpected termination of freeviewer

External Email - Use Caution I see, it works fine when I source freesurfer and then load freeviewer from the terminal. Thank you Andrew for your help. Much appreciated, Lykke 14 feb. 2019 kl. 22:10 skrev Hoopes, Andrew mailto:ahoo...@mgh.harvard.edu>>: You need to load freevie

Re: [Freesurfer] fcseedcor_multiple runs

Dear Freesurfer experts I have asked this question before and I really do appreciate if you could please reply whenever you had a chance. I have been doing seed to seed connectivity analysis using fcseedcor. I have multiple runs for each subject, and based on the fcseedcor help, I am supposed

Re: [Freesurfer] mris_preproc error: dimension mismatch

The subject surface probably changed since the last time you ran qcache and now has a different number of vertices. Try re-running qcache for those subjects. On 2/15/19 2:58 AM, Peters, Douglas G wrote: External Email - Use Caution Hi Everyone, I'm trying to prepare my Cerebral blood f

Re: [Freesurfer] Cortical thickness values extraction issue

This can happen if the label is small and/or you've used a lot of smoothing. It is better to do this kind of thing in fsaverage space rather than moving the labels back to the individual space. If you've run mri_glmfit-sim, then it should have created a table file (something.y.ocn.dat). This fi

Re: [Freesurfer] dt_recon error MatrixReadTxT: could not scan value [1][1]

Can you do this in two steps? First, convert the dicom to a volume format (eg, mgz or nii.gz) with mri_convert image001.dcm dwi.nii.gz This may or may not create bvals and bvecs. If not, then you will have to supply them. If they are created, look at them and make sure they are right. Next ru

Re: [Freesurfer] mri_surf2surf QC

Hi Stephanie I guess visually. You can write a script to run freeview and save a snapshot using something like: foreach s ($SUBJECTS) freeview -f ... -ss then you can zip through them in nmovie (or nmovie_qt, which I guess is what we support now) cheers Bruce On Fri, 15 Feb 2019, Winkel

[Freesurfer] mri_surf2surf QC

External Email - Use Caution Hi Freesurfers, I ran mri_surf2surf and registered self-created parcels from fsaverage to all my subjects. What is the best way to do QC and check if everything went right? Thanks for your help! Stephanie The information contained in this electron

Re: [Freesurfer] extracting mesh file of layers in ascii format

Hi Atena mris_convert wiil convert any surface to ascii if the output file name. For example mris_convert $SUBJECTS_DIR/$subject/surf/lh.pial \ $SUBJECTS_DIR/$subject/surf/lh.pial.asc while convert the pial surface to ascii format. We don't generate mesh representations of the boundaries

Re: [Freesurfer] automatically save the selected plane

Hi Sadia can you elaborate what you are trying to do. What seleected plane? cheers Bruce On Fri, 15 Feb 2019, Sadia Sheikh wrote: External Email - Use Caution Dear FreeSurfer experts It is possible to automatically save the selected planes or set of planes from the speci

Re: [Freesurfer] Fix topology correcting defect

Hi Milène did you edit in freeview? Or something else? If you load the wm.mgz on top of the norm.mgz, does is still look to be in the same space? If so, feel free to tar and gzip the entire subject dir and upload it and we will take a look cheers Bruce On Fri, 15 Feb 2019, Milene Buerger

[Freesurfer] extracting mesh file of layers in ascii format

External Email - Use Caution Hi, How can I extract the mesh file of gray matter, white matter, Cerebellum and Thalamus from freesurfer in Ascii format? Thanks in advance! BR, Atena ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard

[Freesurfer] dt_recon error log

External Email - Use Caution Hello, running the following command line script for dt_recon dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/image01.dcm --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon MatrixReadTxT: could not sc

[Freesurfer] Cortical thickness values extraction issue

External Email - Use Caution Hi FS experts, I did group-level, surface-based, vertex-wise analysis for baseline and longitudinal data. I used Qdec and do the same work with the fsgd version (mri_glmfit-sim command) to double-check the data. I created label files with tksurfer for

[Freesurfer] automatically save the selected plane

External Email - Use Caution Dear FreeSurfer experts It is possible to automatically save the selected planes or set of planes from the specific region? Since I have a large number of data and I want to save all the planes that lie in the midbrain region. Regards Sadia Research S

Re: [Freesurfer] Fix topology correcting defect

External Email - Use Caution Thank you Bruce for your answer! I figured out how to edit the wm.mgz. Indeed some parts of the skull were not properly removed from the brainmask and therefor considered as white matter. I manually removed voxels from the wm.mgz and then I tried to rein