Re: [Freesurfer] Checking raw dicom files

Did you compare the number of slices to that of your sequence? I have had issues when overzealously pulling data off of bourget (that is before the files have completed being sent). A simple re-conversion to mgz (or whatever format you prefer) has fixed this when waiting a bit longer till bourget

[Freesurfer] mri_ms_fitparms_questions

I have run mri_ms_fitparms (version 5.1.0) on phantom data from two multiecho flash volumes (5 and 20 degrees with 8 echos: 1.67ms - 14.83ms in 1.88ms steps) at 7T utilizing a b1 map for correction. How does mri_ms_fitparms know the field strength (I can't figure out where the information is when

Re: [Freesurfer] mri_ms_fitparms_questions

On Thu, 25 Apr 2013, dgw wrote: I have run mri_ms_fitparms (version 5.1.0) on phantom data from two multiecho flash volumes (5 and 20 degrees with 8 echos: 1.67ms - 14.83ms in 1.88ms steps) at 7T utilizing a b1 map for correction. How does mri_ms_fitparms know the field strength (I can't

[Freesurfer] sig.nii.gz

Hi, I am trying to compare the quality of fMRI data with different artifact inducing objects in the magnet. I ran expanding and contracting rings and followed the retinotopy fsfast analysis in FreeSurfer 5.1.0. I am trying to compare the data by looking at the sig.nii.gz (which from the website

[Freesurfer] dimensions of sig.nii.gz

Hi, I am examining the difference in significance between different scan parameters in a retinotopy experiment and analysis. I have loaded the sig.nii.gz file in matlab using MRIread, and I am confused by the dimensions of the volume. I understand that this is a surface based file, but the

[Freesurfer] retinotopy betas

Hi, I am examining the affect a metal artifact has on fMRI data, and I am using Eccentricity mapping with the retinotopy analysis in FSFast. I was recently asked to switch from examining the difference in the fsig to examining the difference in the betas. I opened up beta.nii.gz and I can see

[Freesurfer] retinotopy betas

Hi, I am examining the affect a metal artifact has on fMRI data, and I am using Eccentricity mapping with the retinotopy analysis in FSFast. I was recently asked to switch from examining the difference in the fsig to examining the difference in the betas. I opened up beta.nii.gz and I can see

[Freesurfer] qdec

Hello, I sent the message below yesterday. I can confirm that I am also having problems visualizing with qdec using the standard nmr center install over nx. Everytime I click generate stats table, I get the error below. Is there a non-gui version, which I can use? Does anyone have a way to use

[Freesurfer] contrast question

Hi, I have a quick contrast question. If I don't want to regress out one of my variables for a contrast how do i set that up in a contrast file? For example fsgd: Class a Class b Class c Class d Class e Variables age mmse Input s1 a 23 30 Input s1 b 25 21 Input s1 c 29 25 Input s1 d

Re: [Freesurfer] contrast question

, and mmse slope. I'm not sure what you are trying to do. Do you want an F-test to test whether the groups differ on intercept OR age OR mmse? On 02/25/2014 03:48 PM, dgw wrote: Hi, I have a quick contrast question. If I don't want to regress out one of my variables for a contrast how do i set

[Freesurfer] fsgd plots 2 Class

Hi, What is the best way for me to either generate fsgd plots or at least extract the data when I have 5 classes in my fsgd file (using FS 5.3.0)? I have tried the Plot fsgd option in freeview, when viewing results, but I get a segmentation fault (I assume this means that it isn't supported, but

Re: [Freesurfer] QDEC bad fd number

Are those subjects in your SUBJECTS_DIR? What is the output of ls $SUBJECTS_DIR ? On Tue, Mar 4, 2014 at 1:10 PM, Mihaela Stefan mikaelastep...@gmail.com wrote: Hello, I am re-posting this since I haven't got an answer yet. Thanks! Mihaela On Fri, Feb 21, 2014 at 3:55 PM, Mihaela Stefan

Re: [Freesurfer] QDEC bad fd number

as /usr/local/freesurfer/subjects but I have my working folder in a different location. Could that be the problem? On Tue, Mar 4, 2014 at 1:34 PM, dgw dgwake...@gmail.com wrote: Are those subjects in your SUBJECTS_DIR? What is the output of ls $SUBJECTS_DIR ? On Tue, Mar 4, 2014 at 1:10 PM

Re: [Freesurfer] Extracting thickness, area and folding values from Qdec

I think Doug meant the 1.3. Therefore the line should be something like: mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache 1.3 --sim-sign neg What exactly did you type? (try separating it with lines instead of quotes) HTH, D On Mar 13, 2014, at 6:22 PM, Dusan Hirjak wrote: Dear Doug,

Re: [Freesurfer] Coomand not found

Francesca, Is this a dual boot system (do you have multiple operating systems installed on it)? Are you running FreeSurfer in a virtual machine? It sounds like another operating system may be controlling the permissions of the /media/Shared_Data directory. D On Wed, May 14, 2014 at 9:51 AM,

Re: [Freesurfer] how to get scalp-cortex diff instead of white-pial diff?

Hi, Please see responses in text (also FS experts please fill in on the things I am unsure of). On Tue, May 20, 2014 at 5:09 PM, Christopher Chatham chath...@gmail.com wrote: Dear Freesurfer experts, I would like to get a map of scalp-cortex distance for every vertex on the pial surface

Re: [Freesurfer] URGENT: Error in analyse

Your subject name is wrong. You are saying the subject name is: 54987500 While it is actually: 54987500_output You should either change the name of the SUBJECT directory or change the subject id you are giving to mri_glmfit. HTH D On Wed, May 28, 2014 at 5:17 PM, Saloni Sharma

Re: [Freesurfer] Fwd: How to improve/fix TKMEDIT lag

Hi, What machine are you actually running tkmedit on? more specifically: You appear to be using a mac. Do you run tkmedit directly on the mac? or are you using ssh -X (or something like it to run it) on the Red Hat machines? Thanks, D On Tue, Jun 3, 2014 at 11:55 AM, Vy Dinh vdi...@wisc.edu

Re: [Freesurfer] Displaying subset of labels on template

You could use mri_annotation2label Then just load only the labels you care about. HTH D On Wed, Jun 11, 2014 at 3:11 PM, nmw njmed...@illinois.edu wrote: Greetings, Is there any way to display just a subset of cortical labels onto one of the Freesurfer template brains (e.g., cvs_avg35)

[Freesurfer] fsfast preproc question

The volume produced from the -mni305 option in preproc-sess, does not look like a brain (it seems to be mostly cerebellum. I have attached an image). Is this the expected behavior? I have included the relevant path and information below: source

Re: [Freesurfer] (no subject)

Hugh, Can you provide some examples of the problem with the terminal having issues detecting the FreeSurfer folder (ls pwd etc.)? And describe where the folder is installed on your computer in the Finder? Thanks, D On Mon, Jul 14, 2014 at 12:54 PM, Hugh Pemberton hughpembert...@gmail.com

[Freesurfer] eccentricity and polar maps?

Hi, I am trying to process a small amount of retinotopy data. I have one run of positive polar stimuli with 64 second cycle and another of positive eccentricity data with a 64 second cycle (I realize that I could use better parameters). I have followed the tutorial on

[Freesurfer] mri_convert feature request?

Hi, I'm not sure if this is a bug report or a feature request. I have been using mri_convert to convert dicoms to nii.gz and mgz files, and I have noticed some discrepancies when reading the volumes in with MRIread in either matlab or octave. The volumes differ in their support of the flip angle,

Re: [Freesurfer] mri_convert feature request?

? I'm not sure it does. I suspect that 50 is correct and not 50.00745058060 (can you imagine setting that on the console)? On Tue, 28 Aug 2012, dgw wrote: Hi, I'm not sure if this is a bug report or a feature request. I have been using mri_convert to convert dicoms to nii.gz and mgz files

[Freesurfer] mri_ms_fitparms?

Hi, From the wiki (http://www.freesurfer.net/fswiki/mri_ms_fitparms), I can see that mri_ms_fitparms can accept and afi map. Can someone tell me what assumptions the -afi subcommand makes about the position of the afi map relative to the flash volumes? does it calculate everything in scanner

Re: [Freesurfer] mri_ms_fitparms?

estimation took 0 minutes and 56 seconds. On 10/10/12, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: you need to register them. cheers Bruce On Wed, 10 Oct 2012, dgw wrote: Hi, From the wiki (http://www.freesurfer.net/fswiki/mri_ms_fitparms), I can see that mri_ms_fitparms can accept and afi

Re: [Freesurfer] FW: FreeSurfer remote access question

Did you already try the suggestions on?: http://surfer.nmr.mgh.harvard.edu/fswiki/RemoteAccess Dan On Thu, Nov 8, 2012 at 3:04 PM, Li, Hua hl...@partners.org wrote: Hello, We recently installed freesurfer on an Ubuntu 12.04 workstation for doctors in Emergency room which will be used

Re: [Freesurfer] downloading GradientUnwarping

Is it not included in your freesurfer installation? To check: After sourcing Freesurfer type which grad_unwarp HTH Dan On Thu, Dec 20, 2012 at 9:42 AM, John Drozd john.dr...@gmail.com wrote: Hello, I would like to download and install the software described at

Re: [Freesurfer] head/face surface extraction

Hi Luzia, There is also a script called mkheadsurf, which will generate a high resolution very accurate surface (not restricted by the same spherical restrictions the BEM surfaces have). It may shrink the surface slightly (by 1 - 2 voxels, but it should work). A description of how we use it in

Re: [Freesurfer] freesurfer license file

https://surfer.nmr.mgh.harvard.edu/registration.html On Sun, Feb 19, 2012 at 4:55 PM, Christopher Bell christopherbell2...@gmail.com wrote: How do I obtain a freesurfer license file? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable

Hi Ian, This is a bug in the CBU's freesurfer wrappers written at the CBU site and not a FreeSurfer bug. Ask them to look into fixing it. Basically, the wrapper doesn't transfer all the variables necessary for FreeSurfer to run properly. The only work around for you at the moment would be to

Re: [Freesurfer] mkheadsurf and smseghead

Hi Will, I noticed this as well. I don't know Doug's thinking, but I suspect it was just to avoid generating lots of files. The new script overwrites the lh.seghead, when smoothing. I would just update your script to use lh.seghead instead of lh.smseghead. HTH D Will Woods wrote: Hi, In

[Freesurfer] V1_average missing lh.white rh.white

Hello, I am using FreeSurfer 5.1.0. When running recon-all -label_v1 -s $SUBJECT It could not find the rh.white and lh.white surfaces. Subsequently, there was no data in the rh.v1.predict.label. % tksurfer.bin: no data in label file

Re: [Freesurfer] grid overlay?

If you don't want it to go into the folds of the sulci, you may want to use the brain surface from mri_watershed (note you will have to re-run with --save). This option is probably the simplest and most straightforward. If you are unhappy with those results there are many other options, which

Re: [Freesurfer] grid overlay?

sorry, it should have said -surf -useSRAS options Bruce Fischl wrote: Hi Phiroz, I'm not sure I understand, but I think what you could do is create a volume representation of the grid, then sample it onto the surface with mri_vol2surf cheers Bruce On Fri, 6 Apr 2012, Phiroz

Re: [Freesurfer] FreeSurfer NVIDIA card drivers with CentOS 6.5

Just to add. If you are not using the CUDA options (which in my understanding aren't being updated anyway), I find that the gpu included in modern Intel cpus is more than sufficient for my FreeSurfer and MNE uses. HTH D On Fri, Aug 22, 2014 at 4:15 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote:

Re: [Freesurfer] FreeSurfer NVIDIA card drivers with CentOS 6.5

Hi Tommi, That is true, but it is also the most extreme comparison possible. A crude estimate of the ranking of drivers would be: NVIDIA Intel (these are open source by default) AMD radeon (open source amd) Nouveau (open source nvidia) While both NVIDIA and AMD hardware are of similar speed

Re: [Freesurfer] watershed surface to volume rendering repost

Hi Matt, Did you try the -c option described in the function's help? HTH D On Thu, Sep 4, 2014 at 3:30 PM, Sherwood, Matt matt.sherw...@wright.edu wrote: Bruce, Thanks for the pointer. What is happening is we would like to combine the skin/skull/CSF volumes with that of the cortical

Re: [Freesurfer] make movies of non eeg/meg temporal data ?

Hi Greg, I would use MNE either the C, MATLAB, or python code. All are able to create STC (surface time course) files. You can then generate movies using either the C code or the python package (feel free to post follow-up questions on the mne_analy...@nmr.mgh.harvard.edu list). D On Tue, Sep

Re: [Freesurfer] Issues launching tksurfer

Hi Claire, How did you install FreeSurfer? Did you follow the instructions here: http://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall ? HTH, D On Wed, Oct 15, 2014 at 4:02 AM, Claire Morley clairemorley2...@u.northwestern.edu wrote: Good Morning, I have a quick question regarding the launch

Re: [Freesurfer] FreeSurfer graphics requirement

This is currently a topic of many questions on the list etc. I also have plans (once I get my hands on some hardware, to do some systematic tests, but these will not be happening soon). With well updated intel linux (I assume you are talking about running linux natively on your laptop) drivers,

[Freesurfer] FS-FAST par file ?

If I have events which precede the first MR volume, can I input negative values in my par file? I understand my power, and the advantage of doing this will be minimal, but I wanted to inquire if FS-FAST is capable of handling this case. Thanks, Dan ___

Re: [Freesurfer] retinotopy in subject volumetric space

Hi Ben, You should be able to map it back with mri_surf2vol. I haven't done this, but the wiki page looks fairly detailed: http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol HTH D On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman benjamin.zimmerm...@gmail.com wrote: Hi all, FsFast has

[Freesurfer] viewing question

Hi, In freeview, when I load a volume the voxels are not square to the viewing windows. Is there an option to view the data with the voxels square to the viewing windows? Thanks, Dan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] 'current' FSL

It may help to provide a bit more context e.g. the email/instructions you where you found the reference to 'current' fsl version? HTH, D On Tue, Mar 31, 2015 at 3:31 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Other than someone's recollection, there is probably no verifiable means for

[Freesurfer] fs-fast temporal snr

Hi, Does FS-FAST perform any temporal SNR calculations on data? If so, how. Thanks, Dan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is

[Freesurfer] selxavg3-sess svd NaN error

Hi, I am having a problem running my selxavg3-sess using Freesurfer 5.3.0 stable. I am getting the following error: Saving X matrix to /autofs/cluster/neuromind/dwakeman/mm/subjects/nmr00904/sycabs/sycabs_lh/pr014/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond

Re: [Freesurfer] Installing FreeSurfer on Fedora 21

Ranjan, You may want to try installing it on a local hard disk. Do you have any scratch space you can use on the computer? HTH, D On Tue, Apr 14, 2015 at 5:09 PM, Ranjan Maitra maitra.mbox.igno...@inbox.com wrote: Nick, Thanks! It does match in the gzipped tarball: ~$ md5sum

Re: [Freesurfer] Inflated.nofix has holes!!!

Hi Hassan, You should probably start by working through the tutorials: https://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials This one covers that specific topic. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview hth d On Tue, Jun 9, 2015 at 12:32 PM, Hassan bakhshi

Re: [Freesurfer] Read .mgz file matlab

What command did you type? On Wed, Jun 10, 2015 at 5:32 PM, Mohammed Goryawala mgory...@fiu.edu wrote: Hello All, I am trying to read .mgz files into matlab on MacOSX using the MRIread command. It returns me the following error: SWITCH expression must be a scalar or string constant.

Re: [Freesurfer] Processing problem in Freesurfer

Hi Guo, Simply run recon-all again and add the flag -cw256. Then load up the orig.mgz and make sure the head is fully visible. HTH D On 7/1/15 9:48 PM, 宾果 wrote: Dear Freesurfer team: I am here want to ask for your help for some problems in Freesurfer when I was processing my

Re: [Freesurfer] (no subject)

click on the link at the bottom of every post, or go to the mailing list link on the wiki: http://surfer.nmr.mgh.harvard.edu/fswiki this link on that page: http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer hth d On Thu, Jul 2, 2015 at 8:57 AM, Mojdeh Zamyadi mojde...@gmail.com wrote:

Re: [Freesurfer] Dev Version

Did you check the permissions? You have to make sure the permissions are executable. HTH D On 5/26/15 6:33 AM, Hassan bakhshi wrote: Hi I downloaded the centos 6 freeview.bin and replaced it into $freesurferhome/bin/freeview.bin but now i cant open freeview, it says that it is not a

[Freesurfer] retinotopy polar

Hi, I am setting up a polar angle stimulus program, and I am wondering if there is an option in FS-FAST to analyze data with two opposing wedges for the polar mapping. Participants can keep fixation better with this setup, which is why we are aiming to use it. Thanks, Dan

Re: [Freesurfer] mri_deface

Hi Jürgen, Personally, I don't think defacing is necessary for most DTI data. Assuming your slices don't cover the face (which most DTI data doesn't include), I think you are safe to say the data is inherently defaced. Others may have other ideas. hth d On 8/7/15 6:53 AM, Jürgen Hänggi

Re: [Freesurfer] hello freesurfer developer~

Hi A-reum, I think you may be able to get a faster response if you include some details about your setup: I would start with the following: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting and run bugr. hth D On 7/26/15 5:17 PM, A-reum Min wrote: Hi, Bruce When i use a Qdec, this

Re: [Freesurfer] unpack error

Was there an error during scanning? The error message looks like there was an error during that run and the scan was either aborted by the scanner or the scanner crashed on that sequence. Did you check your lab notebook? hth d On 7/25/15 2:43 PM, Park, Jung Mi wrote: Hi Freesurfer team I

Re: [Freesurfer] paradigm file

Hi Thuc, For similar reasons, I program all of my stimulus programs to write a par file for each run. I recommend you program your stimulus program to do the same. HTH D On Fri, Jul 24, 2015 at 8:12 AM, Thục Trinh thuctrinh...@gmail.com wrote: Hi, In our experiment, one onset trial will be

[Freesurfer] FSFAST -per-run question

Hi, I know that -per-run is the recommended motion correction option, and that it uses the middle frame as the reference for motion correction for each run. I was wondering, if there is a reference, or explanation as to why that was chosen and not some other timepoint. Thanks, d

Re: [Freesurfer] Head circumference

Hi John, There is nothing, which I can think of. What do you want the head circumference for (perhaps we can get you a different measure, which will help)? hth d On Sat, Oct 24, 2015 at 2:22 PM, John Anderson wrote: > Dear FS experts, > I want to inquire if there is

Re: [Freesurfer] Drawing a circle around a vertex on a surface

The only code I am aware of for doing this is in mne-python. hth d On 11/8/15 5:36 PM, Reza Rajimehr wrote: > Hi, > > I want to draw a circle around a vertex on the smoothwm or pial surface, > with a particular radius (e.g. 10 mm), fill the circular region and save it > as a label file, then

Re: [Freesurfer] Mac Version and Output differs

Dear Kasper, This is due to the different operating systems you are running not differences in the computers. Your iMac is running ~10.7 and your MacPro is running ~10.9. You should always run your analysis on the same operating system, however you should get no differences on different computers

Re: [Freesurfer] How can I convert Martinos Center dicoms to the dicom format that dcm2niix recognizes?

Hi Emad, The only problems, which I have run into is major weaknesses in dcm2nii: 1. You must have write permissions on the directory the files are located in. 2. dcm2nii cannot work on symbolically linked files. Therefore, first copy the files to your own analysis workspace: e.g. /cluster//

Re: [Freesurfer] Viewing vitamin E capsules?

Why not just open the T1.mgz and load the FreeSurfer surfaces? Is there a more specific goal? hth d On 10/19/15 10:56 AM, Hutton, Seth wrote: > Dear users, > > I have been using FreeSurfer for a while now, but am working in a new > lab and their goals fall outside of my realm of experience. >

Re: [Freesurfer] Error Messages for Accessing Bin

--x 1 tle7 stanford 1672136 Aug 15 2010 > /home/tle7/freesurfer/bin/mri_convert > tle7@sni-vcs-gotlib:~$ > > > On Fri, Oct 2, 2015 at 10:39 AM, dgw <dgwake...@gmail.com> wrote: >> >> Timothy, >> >> What is the output of this command: >> >>

Re: [Freesurfer] Large SA when using pial surface...?

Niels, Why do you expect the surface area to be the same between the two different surfaces pial, and white? hth d On Fri, Aug 28, 2015 at 8:23 AM, Gerrits, Niels n.gerr...@vumc.nl wrote: Dear Experts, With your help, I recalculated the surface area, now using the pial surface instead of

Re: [Freesurfer] Did not find any volume geometry information in the surface

Eric, It will be easier to help, if you provide a much more detailed description of what you did: the full command line, the version of freesurfer, and all terminal output (http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting this may help). hth D On Mon, Aug 31, 2015 at 3:27 PM, Erik Lindberg

Re: [Freesurfer] Questions about the correction methods in Surfstat

Hi Feng, This is not the surfstat list. You may want to check their webpage to see how to get help and documentation. hth d On Sun, Sep 13, 2015 at 9:36 AM, chenhf_uestc wrote: > Dear Surfstat Users, > > I have a question about the RFT correction method in the >

Re: [Freesurfer] freeview crash with emutls_get_address but work from command line on MacOS X 10.10.5

Starting Freeview from MATLAB is an odd thing to do. What happens if you just start freeview normally? hth D On Tue, Sep 15, 2015 at 12:21 PM, Knut Jørgen Bjuland wrote: > When I load Freeview developmental version from Freesurver developmental > version from Matlab

Re: [Freesurfer] freeview crash with emutls_get_address but work from command line on MacOS X 10.10.5

R correction that uses > data from both hemisphere. I have managed to get it working under Ubuntu > 14.04.3. > > > > On 15 Sep 2015, at 18:49, dgw <dgwake...@gmail.com> wrote: > > Starting Freeview from MATLAB is an odd thing to do. What happens if > you just start freeview n

Re: [Freesurfer] Error using selexavg3-sess

Hi Keji, Without more details, it may be hard to guess. I suspect it might be that not all of the conditions in your analysis happened during the experiment for those participants (e.g. some sort of button press). hth d On 10/2/15 5:47 PM, Morenikeji Adebayo wrote: > Just following up on this

Re: [Freesurfer] White Matter Edits vs. Control Points, & third party software

Alberto, I included detailed replies below, but I have a question before you get to those. Why don't you want to follow the FreeSurfer techniques for reconstruction? You suggested several other ways, but I don't understand your motivation for not wanting to follow the instructions for

Re: [Freesurfer] Error Messages for Accessing Bin

Timothy, What is the output of this command: ls -l /home/tle7/freesurfer/bin/mri_convert ? hth d On Fri, Oct 2, 2015 at 1:36 PM, Timothy Quang-Tin Le wrote: > Hi, > I tried the chmod command, but it did not work. How I check that I've > downloaded the correct version? >

Re: [Freesurfer] searchable Destrieux atlas by recon all labels?

question: is there truly no interactive, online atlas > that uses either the Destrieux or Duvernoy parcellation scheme to examine > the landmark boundaries with respect to, say, MNI space? > > Thanks, > Andrea > > On 1/7/16, 4:26 PM, "dgw" <dgwake...@gmail

Re: [Freesurfer] searchable Destrieux atlas by recon all labels?

freeview partial solution If this is important to you, you could write a quick script to do this for you: 1. mri_annotation2label to output all labels 2. write a script to launch freeview and load all of the labels (reading the color and applying it from the FS ctab file) e.g. freeview -f

Re: [Freesurfer] mri_convert segfault error

. >>> ls -l ../ >>> >>>> ... >>>> drwxr-xr-x 13 myuser myuser 4096 Jun 2 11:50 mri >>>> ... >>>> >>> >>> - >>> Joshua Lee, Ph.D. >>> Post-Doctoral Researcher >>> MIND Institute >&g

Re: [Freesurfer] Fwd: Getting the pial surface to cover the entire medial temporal lobe structures

I would try Bruce's idea first, but another option would be to run mri_tesselate on the aseg volume you had loaded in those images. hth d On Wed, Jun 15, 2016 at 4:46 PM, Bruce Fischl wrote: > Hi David > > we don't have anything that does this by default, sorry. If

Re: [Freesurfer] (no subject)

Jasmin, Did you follow the instructions from the wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall which links to this mac specific page. https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall ? hth d On Thu, Jan 14, 2016 at 5:10 PM, Jasmin Alves wrote: >

Re: [Freesurfer] comparing multiple runs on the same scan

Doug responded to your previous mail with this: Even on the same operating system they will be different because there is stuff in the header that will change. Use mri_diff (volumes, segmentations, and surface overlays) or mris_diff for surfaces to check whether they are different. hth d On

Re: [Freesurfer] Viewing nifti file in freeview

Amanda, Is there a progress bar still running? Have you tried changing the window min max fields? hth d Sent from my Phone > On Feb 4, 2016, at 06:46, Worker, Amanda wrote: > > Hi All, > > > I was hoping someone could help with an issue that I'm having that I'm

Re: [Freesurfer] Zero angle for retinotopy

Hi, I know Doug is away, so he may correct me later, but I believe it doesn't matter, as long as it is consistent across runs, and you know what it is. It will just determine where the angle 0 activity goes (in a color map etc.). The way FS-FAST does the mapping it just may mean your colors don't

Re: [Freesurfer] spot checking results

Don, Running FreeSurfer on two different versions of any operating system will not produce the same results. If you want the same results, you must use exactly the same version of an operating system for all of an analysis. hth d On 2/5/16 8:29 PM, Krieger, Donald N. wrote: > Dear List, > >

Re: [Freesurfer] Segmentation depends on image file format

What software did you use to generate the NIFTI files? Many of the converters do different things to the axes of the data, and this does affect results. hth d On Thu, Jan 28, 2016 at 8:49 AM, Parzer, Peter wrote: > Hi, > > we have brain images stored as DICOM

Re: [Freesurfer] Fwd: Creare Annot File in Freesurface

try specifying the full path to the label. hth d On Wed, Feb 24, 2016 at 2:37 PM, Faeze Vedaei wrote: > Hil Freesurfer experts, > > I am trying to create annot file in freesurface using mris_label2annot > command. In this process, I got an error : cannot find or read >

[Freesurfer] mri_label2vol projfrac missing voxels

Hi, I am having trouble with the projfrac option in mri_label2vol (on the current dev freesurfer environment). When I use the following command: mri_label2vol --annot label/lh.lang.annot --subject nmr00937 --o lang_seg.mgz --hemi lh --identity --temp mri/T1.mgz --proj frac 0 1 .01 I get many

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi Faeze, I believe the name comes from the Color LUT file. Try changing the name in there. hth d On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei wrote: > Hi Freesurfer experts, > > I have created an annotation file by several label files using > mris_label2annot command

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi Faeze, It is difficult to help without more details, but in my experience, (exact command, the color lut file in text in the email and what the error in the naming was, which label went to which entry in the color lut.) You need to put the labels in the order of your custom color lut file.

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi Faezeh, Can you send these in the text of the email. It is very hard to deal with these files? The LUT file shouldn't be an excel file it should be a plain text document (please attach). Thanks, D On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei wrote: > Hi > > Thank you

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi Faezeh, Please provide more details (those i described in the earlier email). Thanks d On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei wrote: > Hi, > > I checked again to arrange the labels in the order of LUT file, but the > result has not changed. Can you help me more

Re: [Freesurfer] (no subject)

Maheen, it sounds like a question that could be better answered by the Homer2 list. hth d On Fri, Feb 26, 2016 at 8:13 AM, Maheen Siddiqui wrote: > Dear FreeSurfer Users, > > I have a head surface mesh and a pial surface mesh obtained after > segmentation of a T1

[Freesurfer] separate non-contiguous labels

Hi, I want to separate each label in the Yeo parcellations into each of their separate contiguous labels. Is there a command, which can do this in Freesurfer? Example lh.yeo7.annot the network 7 label has 5 non-contiguous components Is there a command to separate these into 5 separate labels?

Re: [Freesurfer] abnormal inflated surface

Hi Jasmin, nothing looks wrong with the inflated brain images to me. Remember, the inflated brain doesn't have the same space as the T1 or white matter surface, so they are just centered. And overlap one another as the slice views showed. I'm afraid I can't help with the hippocampal question,

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi Faezeh, Please run the exact commands including the file I attached, not the aparc.annot.a2009s.ctab, and check the result using the freeview command I provided. Then let me know what label freeview shows. hth d On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei wrote: >

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

yes, just follow the pattern of the file. You will probably want to use different RGB values to get different colored labels. hth d On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei wrote: > Hi, > > I should let you know that, it works! It shows paracentral name in tksurfer. >

Re: [Freesurfer] mri_label2vol projfrac missing voxels

clut file. hth d On Mon, Feb 29, 2016 at 2:16 PM, dgw <dgwake...@gmail.com> wrote: > Hi, > > I just wanted to repost this question. After turning on the > transparency, I also noticed that this problem goes both directions > (i.e. some voxels which aren't gray matter

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

It is just a text file (you can open it with vi or gedit whatever), just add new lines for new labels and make the colors the color you want them to be.\ hth d On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei wrote: > Thank you so much for you response. I should say that I

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi Faezeh, Check this page out for details. The values are just numbers in the columns of the file: https://en.wikipedia.org/wiki/RGB_color_model hth d On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei wrote: > Hi, > > I really appreciate you for help me in this process. May

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

The 4 number columns represent: Red Green Blue and Alpha The numbers range from 0-255. They can be combined to create any color. Play around, and you will see what it does. hth, d On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei wrote: > Hi, > > Thank you so much for you

Re: [Freesurfer] System crash by extremely much generated output v6 beta-Repost

20 GB is not a lot for a full macos install + data, how much room was free before you ran recon-all? What is the hardware? CPU, RAM etc. hth d On Wed, Mar 9, 2016 at 12:09 PM, Gronenschild Ed (NP) wrote: > Hi developers, > > Could you please help me out

Re: [Freesurfer] System crash by extremely much generated output v6 beta

Hi Ed, I am a bit confused by your two emails. In one you state that you have a MacPro OSX10.7 installed on a partition of 20 GB with FreeSurfer v6 beta Then in the next post you state that the disk you have is 1.5TB (is that the disk or partition?) I'm also confused, because you stated that

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