[Freesurfer] tracula bvecs problem

Dear Freesurfers. I am trying to run trac-all on one subject and have a problem with the bvecs file at the -prep stage. After dtifit is started an error massage occurs: Error: bvecs and bvals don't have the same number of entries. I checked the dmri/bvals and dmri/bvecs. There seems to be a prob

[Freesurfer] weird fieldsign image

Hi All, I am running a retinotopy analysis, and when I look at the fieldsign image all I see are a bunch of red and blue speckles. Is this normal? I am trying to figure out the horizontal and vertical meridians and am not sure how to use the fieldsign image to do this. It's for my thesis, i

Re: [Freesurfer] Fwd: freesurfer recon error

Have you tried including the flag -cw256 with the recon-all command? On Tue, Jul 5, 2011 at 10:18, Sarah Rappaport - UoB` wrote: > Hi!, > > I am new to FreeSurfer and I am having some difficulty with the T1 > reconstruction. My MRI files were Par Rec and converted to nii. I > successfully conver

Re: [Freesurfer] Thickness measurements stats

Hi Ignacio, the thickness is definitely affected by factors such as sequence type, field strength and acquisition parameters (not to mention age, maybe gender, etc...) so I think you need to acquire your own control(s) on a matched acquisition. cheers. Bruce On Tue, 5 Jul 2011, Ignacio Let

Re: [Freesurfer] error using recon-all function

Freesurfer experts, I emailed last week with an error using recon-all. This problem has still not been resolved. The summary of the problem should be shown below: Thanks, Ryan On Fri, Jul 1, 2011 at 2:06 PM, Ryan Hutten < ryanhutten2...@u.northwestern.edu> wrote: > > > -- Forwarded mess

Re: [Freesurfer] Thickness measurements stats

Then, and finally is this method the best way to determine whether exist any cortical thickness anomaly, I mean, to use a normal control acquisition as comparisson? Thanks in advance Ignacio. 2011/7/5 Bruce Fischl > Hi Ignacio, > > the thickness is definitely affected by factors such as sequenc

[Freesurfer] correct mris_anatomical_stats syntax for lgi

Hi FS experts: I have run a group analysis with Local Gyrification Index (LGI) and obtained some statistical significant areas.Now I want to extract the information (lgi) of each area.Based on the QDec Group Analysis page, the following command is ran to examine cortical thickness: mris_an

Re: [Freesurfer] Thickness measurements stats

I can't say whether it's the best way, but it should be relatively unbiased On Tue, 5 Jul 2011, Ignacio Letelier wrote: Then, and finally is this method the best way to determine whether exist any cortical thickness anomaly, I mean, to use a normal  control acquisition as comparisson? Thanks

[Freesurfer] Matlab and FS

Hello FS'users, I'm trying to do an histogram of cortical thickness for 2 cases in matlab, but the problem is that I have Installed matlab in a computer (windows) and FS in another one (ubuntu) Can I configure something to use the FS commands in matlab in order to obtain some graphs? And also, whe

[Freesurfer] Tksurfer Time Course Correlation

Hi, I have a couple of questions about Tksurfer's time course correlation option. First, what type of correlation does it show? Does it use Pearson's r or something else? Second, is there any way to get the same output from the command line? From previous list discussions, it looks like it migh

[Freesurfer] measuring cortical thickness using FreeSurfer

Hi, I am running freesurfer on 64 bit Fedora 10 linux. I am using version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0. Can anyone point me to a reference web page listing what steps I need to type to process a series of MRI dicom slices and use FreeSurfer to measure cortical thickness for

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide On Tue, Jul 5, 2011 at 13:14, John Drozd wrote: > Hi, > > I am running freesurfer on 64 bit Fedora 10 linux. > I am using version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0. > Can anyone point me to a reference web page l

Re: [Freesurfer] Matlab and FS

  Hi Carolina   There is a directory freesurfer/matlab which contains several matlab-based scripts for reading and writing (after modified) surface- and volume-based data generated in freesurfer. Transport files from Linux to Windows will be tedious and things may not work properly, therefore,

Re: [Freesurfer] Matlab and FS

Hi Carolina, the thickness in each region can be obtained either from the aparc.stats file or in matlab by loading the thickness using read_curv.m and the various label files with read_label.m. Make sure to account for the indices being one-based in the return from read_curv.m, but zero-based i

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

recon-all \ -i \ -s \ -sd \ -all cheers Bruce On Tue, 5 Jul 2011, John Drozd wrote: Hi, I am running freesurfer on 64 bit Fedora 10 linux. I am using version:  freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0. Can anyone point me to a reference web page l

Re: [Freesurfer] tracula bvecs problem

Hello again. I dug into the code and could locate the problem (I don't have a solution, though. My coding skills are quite amateurish.) I think the problem somehow lies in the format of my bvecs file. flip4fsl is not able to read it correctly: --- if (-e $inbvecs) then echo "INFO: found

[Freesurfer] fieldsign problems

Hi All, I am running a retinotopy analysis, and when I look at the fieldsign image all I see are a bunch of red and blue speckles. Is this normal? Thanks. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e

Re: [Freesurfer] fieldsign problems

no, it's definitely not normal. Do you see any error messages? Can you explain exactly what you did? On Tue, 5 Jul 2011, Michelle Umali wrote: > Hi All, > I am running a retinotopy analysis, and when I look at the fieldsign > image all I see are a bunch of red and blue speckles. > > Is this norma

Re: [Freesurfer] tracula bvecs problem

Hi Franz, Please refer to the following page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Specifically Step7.2 for the format in which bvals/bvecs files should be given as an input. If your input bvals/bvecs are in the right format flip4fsl should not give you an error. Also if

[Freesurfer] gyrification Index of a label

Hi All, I have run recon-all -s -localGI Now I want to get the gyrification Index of a particular label. Is there a way to do that ? Please let me know Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.har

Re: [Freesurfer] tracula bvecs problem

Hi Franz, Sorry I just saw your previous email now. The problem could be due to the variable decimal places you've used in your input bvecs file. I've modified your bvecs file from the previous email to 3 decimal places constantly for all the gradient values (See Attached!!). Can you check to see

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

Hi Bruce and Pedro, Thank you both for sending me your suggestions. Just to let you know, because my .dcm (dicom) files had a space and two dots in the filenames: (e.g. "2008_12_08.ek -0035-0001-1.dcm" ) (and using quotes around the file name or "\ " within the filename without the quotes did

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

sorry, but the majority of the time is required. We're working to speed things up, but it is complicated software with multiple nonlinear warps, segmentation procedures, etc Bruce On Tue, 5 Jul 2011, John Drozd wrote: Hi Bruce and Pedro, Thank you both for sending me your suggestions.

Re: [Freesurfer] gyrification Index of a label

this command can be used: mri_segstats --annot my_subject_id lh aparc \ --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi \ --sum lh.aparc.pial_lgi.stats i've updated the lGI wiki page to include this as well. n. On Tue, 2011-07-05 at 14:15 -0400, Ritobrato Datta wrote: > Hi All, > > I hav

Re: [Freesurfer] gyrification Index of a label

Hi Ritobrato, Nick already answered your query. Just a small add: the gold standard to use local gyrification index is to compute vertex-wise analyses rather than parcel-wise comparisons. Indeed, lGI at each point already quantifies the gyrification in the surrounding region. As a result, the

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

Hi Bruce, Okay, thank you. I understand and can see that to do an accurate job, the pipeline must be complicated. I have eight processors on my linux desktop computer. Maybe some parts of recon-all are multi-threaded which could speed things up for me :-) Thank you, John 2011/7/5 Bruce Fischl

Re: [Freesurfer] gyrification Index of a label

and to further this, i added a section on the wiki page on how to use qdec to perform a surface-based lgi analysis. basically, you just do this: To perform a vertex-wise analysis in QDEC of the lgi surface data, first sample the results to the average template subject 'fsaverage': recon-all -s

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

Sorry, that won't help a single subject much, although there are options to run the hemis in parallel. You can run multiple subjects at the same time, which is what we usually do. Or you can use cuss On Jul 5, 2011, at 5:11 PM, John Drozd wrote: > Hi Bruce, > > Okay, thank you. I understand

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

Hi Bruce, Thanks for the suggestion, Bruce. I'll run 8 different subjects at once. Take care, John 2011/7/5 Bruce Fischl > Sorry, that won't help a single subject much, although there are options to > run the hemis in parallel. You can run multiple subjects at the same time, > which is what we

Re: [Freesurfer] tracula bvecs problem

Hi Franz - Which of the files that you sent us are the original files (the bvalfile and bvecfile from your dmrirc)? I could not find any files that had 33 lines among your attachments so I'm not sure what your input files look like. Thanks, a.y On Tue, 5 Jul 2011, Franz Liem wrote: > Hello a

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

how much ram do you have? You'll need at least 2G/subject if not 3 On Tue, 5 Jul 2011, John Drozd wrote: Hi Bruce, Thanks for the suggestion, Bruce. I'll run 8 different subjects at once. Take care, John 2011/7/5 Bruce Fischl Sorry, that won't help a single subject much, although the

Re: [Freesurfer] stats on masked functional data

mri_anatomical_stats will do that for you. see mri_anatomical_stats --help it would be something like: mris_anatomical_stats -l ../label/lh.V1.label \ -t ./lh.beta.mgh \ -f lh.beta.stats \ my_subject_id lh note that the column name will say 'ThickAvg' and 'ThickStd', whi

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

Hi Bruce, Thanks for pointing this out to me about the RAM. I have 8 Gb of RAM. So I guess I can safely run 3 or 4 subjects simultaneously if each subject requires 2 to 3 Gb of RAM. Thanks, John Sent from my iPhone On 2011-07-05, at 6:08 PM, Bruce Fischl wrote: > how much ram do you have?

[Freesurfer] calculating the surface area of each region on Desikan template

hi, expert,   How could I obtain the surface area of each region on the Desikan template? How can I obtain this area in both native space and the average template space? In the surf folder of each subjects, I noticed there is lh.area file, what is meaning of this file? Do I need ?h.area for calcul

[Freesurfer] MRI registration

Hi all, I'm trying to register two brain volumes using Freesurfer. I need to find a mapping for each voxel of the MR image to the reference image. I tried using mri_register with the option -vf as the wiki documentation suggests that it outputs a vector field. Instead it expects a variance volume.