[Freesurfer] dwi_orig.nii.gz does not exist

Hi list, I have a strange problem with TRACULA.The analysis run fine on all subjects but on the last two, -prep command produces this error: #@# Image corrections Mon Jul 20 09:09:54 CEST 2015mri_convert $SUBJECT/data.nii.gz $SUBJECT/dmri/dwi_orig.nii.gzcp $SUBJECT/bvecs.txt $SUBJECT/dmri/dwi_or

[Freesurfer] Ubuntu 14.04 LTS 64 bits

Hi: Which freesurfer version must I install in Ubuntu 14.04 LTS 64 bits ?... Sincerely... Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-21051

Re: [Freesurfer] Ubuntu 14.04 LTS 64 bits

The "CentOS 6 x86_64 (64b)" Platform release. Here is a link: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz -Zeke On 07/20/2015 10:10 AM, Gonzalo Rojas Costa wrote: > Hi: > >Which freesurfer version must I install in Ub

[Freesurfer] mri_label2vol change to MNI 152

Hi Freesurfer listserve, I hope you are well. I emailed the freesurfer listserve also but got no response. I am trying to take an functional ROI that is anatomically constrined that I created using tkmedit and transform it to MNI152 space. I saved it as $label.label. Then did this command: m

[Freesurfer] mac installation problems

Hi, I am a new user of freesurfer. I have been running freesurfer on a Linux machine to look at hippocampal subfield volumes, but am now trying to switch over to a mac. I have installed the program, and it is located within /Applications/freesurfer. Ran the freesurfer source and export. When

Re: [Freesurfer] mac installation problems

When you tried recon-all again on subject bert, what was the error message? On 07/20/2015 12:02 PM, Austermuehle, Alison (NIH/NINDS) [F] wrote: > > Hi, > > I am a new user of freesurfer. I have been running freesurfer on a Linux > machine to look at hippocampal subfield volumes, but am now tryin

Re: [Freesurfer] mac installation problems

ndsd-ces-5s205:mr_0007 austermuehleaa$ sudo chmod -R a+w $FREESURFER_HOME/subjects/bert ndsd-ces-5s205:mr_0007 austermuehleaa$ recon-all -s bert -all INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503 Current Stamp: freesurfer-Darwin-lion-

Re: [Freesurfer] mac installation problems

Hi Alison, what are your new errors (the ones you get almost immediately)? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Alison Austermu

Re: [Freesurfer] mac installation problems

As stated in the error message, you need to download a license file. This is required for all machines running freesurfer. Please follow the instructions under the "License" section of the following page: https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac -Zeke On 07/20/2015 1

Re: [Freesurfer] mac installation problems

Hi, Error as follows: ndsd-ces-5s205:mr_0007 austermuehleaa$ sudo chmod -R a+w $FREESURFER_HOME/subjects/bert ndsd-ces-5s205:mr_0007 austermuehleaa$ recon-all -s bert -all INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503 Current Stamp:

[Freesurfer] Correction with white-matter-points

Dear FreeSurfer Team! Last week I wrote about to the mailing list about problems occurring after the WM-point correction. Later I received a message in which You told me that You can help me if I upload the scan. Where and how can I do this? Thank You for Your help! Kind Regards Pawel W. Psyc

Re: [Freesurfer] Correction with white-matter-points

Hi Pawel you should look on the wiki for this type of info! Instructions are here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange cheers Bruce On Mon, 20 Jul 2015, Wrobel, Pawel wrote: > Dear FreeSurfer Team! > > Last week I wrote about to the mailing list about problems occurring a

Re: [Freesurfer] R: R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

On 07/20/2015 02:10 AM, std...@virgilio.it wrote: > Hi list, > > in the previous mail you have suggested to run fcseed-config and > specify -seg ROI_MASK.mgz and -segid 1 (assuming my ROI_MASK is in > $SUBJECTS_DIR/subject/mri). > I have two question please. > A- my mask is on vmPFC, thus it in

Re: [Freesurfer] help with using optseq2

The problem is probably that you have specified a maximum for the null event and it just does not need as much run time (# of time points) that you have allocated. On 07/16/2015 06:17 PM, Heeyoung Choo wrote: > Hello, > > I'm trying to create trial sequences for a slow event related fMRI experim

Re: [Freesurfer] QDEC question

Does /home/anup/Desktop/QDEC/fsaverage/surf/lh.white exist? If not, cd /home/anup/Desktop/QDEC/ ln -s $FREESURFER_HOME/subjects fsaverage It looks like you will have a second problem in that the subject class GenderFemale-DiagnosisSCA1 does not have any members doug On 07/17/2015 08:17 AM, Dr S

Re: [Freesurfer] Multimodal Extraction of Freesurfer ROI Intensity Values

Try mri_segstats. Run with --help for more info and examples doug On 07/17/2015 02:01 PM, Lakhani, Bimal wrote: > Hello, > > To this point, I have been able to successfully register Myelin Water > Fraction (MWF) scans to Freesurfer Base Space in the longitudinal > pipeline (thank you for the hel

Re: [Freesurfer] bad registration using mri_vol2vol

where did lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.mgz come from? It must be in the space of $SUBJECTS_DIR/fsaverage/mri/orig.mgz for that transform to work On 07/17/2015 02:43 PM, Barbour, Tracy,M.D. wrote: > > > Hello, > > I'm trying to convert an ROI mask I created in MNI305 space to MN

Re: [Freesurfer] error in atlas creation

Hello, I was wondering if these got uploaded correctly. Please let me know if I made a mistake and thanks, Anthony On 7/9/15 1:41 PM, Bruce Fischl wrote: > sure > On Thu, 9 Jul 2015, Anthony Dick wrote: > >> Hello Bruce, >> >> I am still getting this error after re-running autorecon1 in the new

Re: [Freesurfer] make_average_subject for subcortical volumes in children

Hi Kristi yes, that is correct. Everything is stored in native space and all processing is done there until you start doing group-level stuff cheers Bruce On Fri, 17 Jul 2015, Kristi Griffiths wrote: Dear FS experts,   I am new to freesurfer and have a few basic questions.   I have

Re: [Freesurfer] help on mris_preproc

Dear Doug, I was away a while and missed your email. I have not resolved this issue yet. Could you please help? Thanks. David -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, Ju

Re: [Freesurfer] help on mris_preproc

I think you have a non-standard directory structure. FS is expecting something like $SUBJECTS_DIR/subject1 but it looks like you have the FS results in $SUBJECTS_DIR/subject1/freesurfer You have to use the FS structure or else it will generate an error doug On 07/20/2015 03:14 PM, David C. Zhu wr

[Freesurfer] Dividing Entire Scan By Intensity Factor & Create Overlay Surface

Hello again and thank you for the continual help! As before, I am continuing down the path of registering/extracting data from Myelin Water Fraction Scans using the outputs from the Freesurfer Longitudinal Pipeline. As the intensity is the main outcome measure of the MWF, I would like to displ