[Freesurfer] Regarding: dlPFC volume

Dear freesurfer experts, I managed to create dlPFC ROI and successfully extracted the cortical surface parameters. I also want to have the whole volume of dlPFC (*not* the gray matter volume). Will it make any sense if I multiply dlPFC ROI surface area with its corresponding thickness to get a

[Freesurfer] Center Director Ad: Umass Amherst Human Magnetic Resonance Center

Please post this ad: Human Magnetic Resonance Center Director (Tenured Associate or Full Professor) The Department of Psychological and Brain Sciences and Institute for Applied Life Sciences at the University of Massachusetts Amherst, invite applications for a tenured faculty position at the

Re: [Freesurfer] (no subject)

Hi Sadhana, this has been answered several times. Are you not getting the replies from the list? On 12/16/16 6:13 PM, Sadhana Singh wrote: Hello FreeSurfer Developers, I'm running the recon-all on my subjects data as described in freesurfer tutorial

[Freesurfer] (no subject)

Hello FreeSurfer Developers, I'm running the recon-all on my subjects data as described in freesurfer tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial), but it shows the following error when I run the recon-all command: ERROR: cannot find CON_101.nii recon-all -s exited with

Re: [Freesurfer] Tracula Set: No Match

It doesn't recognize the format of your field map. It assumes that the field map has either 2 frames (2 phase maps) or 1 frame (a phase difference map). From: Katherine Damme [katherine.da...@gmail.com] Sent: Friday, December 16, 2016 5:18 PM To: Freesurfer

Re: [Freesurfer] Tracula Set: No Match

When I run this on the command line it seems to be completing the fslroi step fine: "fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1 ERROR: Unrecognized format of phase map

Re: [Freesurfer] V6 FS eTICV versus CAT12 TICV with Small Heads

Wow, that’s a terrible correlation between two putative measures of head size. What does the scatterplot of FS’s “eTIV” vs “SupraTentorialVol” look like? The latter is based on the surfaces, so a scatterplot of the two can be a good way to identify cases where the talairach.xfm file (from

Re: [Freesurfer] ERROR: the pixel data cannot be loaded as it is JPEG compressed.

try running dcmdjpeg on it first. This will create a new set of files that you probably want to put in another directory to avoid overwriting your raw data cheers Bruce On Fri, 16 Dec 2016, Warner, Graham Cary wrote: Hi, I'm trying to open a dicom using the center's instillation of

Re: [Freesurfer] License problem

if recon-all works then you must have a license file. Are you sure that FREESURFER_HOME is defined in your environment and points to the right place? That's where we look for the license file (then in /Applications/freesurfer on the mac if FREESURFER_HOME isn't defined in the env0 cheers

Re: [Freesurfer] (no subject)

Hi Sadhana did you not get the responses that Doug and I sent? Ceck to make sure you are giving the actual full file name, with path and with .gz extension (if it has that). Or just give it *one* file in the dicom series directly and don't bother converting to nifti cheers Bruce On Fri, 16

[Freesurfer] ERROR: the pixel data cannot be loaded as it is JPEG compressed.

Hi, I'm trying to open a dicom using the center's instillation of freesurfer (/usr/local/freesurfer/nmr-stable53-env) but get the following error message when trying to load the file. Starting DICOMRead2() dcmfile =

Re: [Freesurfer] (no subject)

Try typing the full path to the CON_101.nii file On 12/16/2016 02:05 PM, Sadhana Singh wrote: > Hello FreeSurfer Developers, > > I'm running the recon-all on my subjects data as described in freesurfer > tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial), but it shows > the

Re: [Freesurfer] License problem

At the current stage I can run recon-all and get the results without problems. If the license would not work I couldn't be able to run it. Can someone send me the type of license file I should generate? In the website it says that I should get a license.txt by email, but I didn't get any file

[Freesurfer] (no subject)

Hello FreeSurfer Developers, I'm running the recon-all on my subjects data as described in freesurfer tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial), but it shows the following error when I run the recon-all command: ERROR: cannot find CON_101.nii recon-all -s exited with

Re: [Freesurfer] License problem

Is the file you created located in /Applications/freesurfer? Also, fir good measure, try creating the same file but naming it .license in the /Applications/freesurfer On 12/16/2016 11:20 AM, Marco Ganzetti wrote: > Dear all, > I am trying to display a volumetric file to a surface using

[Freesurfer] V6 FS eTICV versus CAT12 TICV with Small Heads

Hello everyone! I have some questions about FS eTICV. I read on the Wiki that eTICV is not the best measure of ICV and saw the same from other articles. The alternative I decided on was measuring the TICV using CAT12 from SPM. I decided to do a scatterplot of the eTICV from FS V6 and TICV from

Re: [Freesurfer] Own ROI for cortical thickness measurements

Hi Andreas what to you mean "I already tryed the mri_vol2surf and mri_vol2roi, unfortunately without successs." In what way didn't they work? cheers Bruce On Fri, 16 Dec 2016, andi...@gmx.net wrote: Dear Freesurfer-experts,   I want to create my own ROI for purposes of cortical thickness

[Freesurfer] License problem

Dear all, I am trying to display a volumetric file to a surface using mri_vol2surf and then tksurfer. Here is the error message I get. I have obtained the email with the few license lines to copy in a file (that i created) name license.txt I created a new file and erased the existing LICENSE

[Freesurfer] Own ROI for cortical thickness measurements

Dear Freesurfer-experts, I want to create my own ROI for purposes of cortical thickness measurements in Freesurfer. As input, I have a binary_volume_mask.mgz. But I'm lacking to get this mask as a label or volume into the FS structure. I already tryed the mri_vol2surf and mri_vol2roi,

[Freesurfer] FLAIR T1 misregistration

I am trying to run recon-all with a T1w image and a FLAIR image to improve the removal of the dura. I am using the command recon-all -sd /cenc/mri/freesurfer -subjid 34P1001 -all -i /cenc/mri/subjects/34P1001/freesurfer/input/t1w.nii.gz -FLAIR

Re: [Freesurfer] how to make label from volumetric mask? (Douglas N Greve)

Thank you, that worked perfectly! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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

Re: [Freesurfer] 6.0 release date?

Is there a chance to get Nvidia GPU support with a current library version (7.5 or 8.0)? Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Douglas N Greve Gesendet: Donnerstag,