[Freesurfer] Optimizing FreeSurfer for Mouse brain

External Email - Use Caution Dear Experts, Could you please suggest to me how to optimize FreeSurfer for 3D MRI Mouse Brain analysis? Regards Ramesh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard

Re: [Freesurfer] Error in loading wmparc2diff.mgz

ist? > > On 2/2/2025 11:34 AM, Ramesh Babu wrote: > > External Email - Use Caution > Dear Experts, > > May I know why wmparc2diff is unreadable? Please suggest. > > Thank you > Ramesh > > On Fri, Jan 31, 2025, 9:01 PM Ramesh Babu > wrote: > >&

Re: [Freesurfer] Error in loading wmparc2diff.mgz

External Email - Use Caution Dear Experts, May I know why wmparc2diff is unreadable? Please suggest. Thank you Ramesh On Fri, Jan 31, 2025, 9:01 PM Ramesh Babu wrote: > Dear Yujing, > > For the command, > freeview > /mnt/data_analysis/freesurfer_data/diffusi

Re: [Freesurfer] Error in loading wmparc2diff.mgz

surfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Ramesh Babu > *Sent:* Friday, January 31, 2025 8:19 AM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Error in loading wmparc2diff.mgz > > > > *External Email - Use Caution* > > Dear Yujing,

[Freesurfer] Error in loading wmparc2diff.mgz

External Email - Use Caution Dear Expert, I am finding an error in loading wmparc2diff.mgz in freeview. The error report from the terminal is; $ freeview -v lowb.nii.gz $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green $SUBJE

Re: [Freesurfer] registration error

External Email - Use Caution Thank you Dear Douglas Ramesh On Mon, Jan 6, 2025 at 7:46 PM Douglas N. Greve wrote: > You have to pass it the name of the subject with the --s flag. The subject > name is that produced by recon-all -s subject ... > > > On 1/4/2025

[Freesurfer] registration error

External Email - Use Caution Hello, I want to register JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz with local subject space. For this, I want to generate a registration.dat file which will be used for registration with local subject image. But I am facing an issue which I pasted below

Re: [Freesurfer] Error in dt_recon

; recon-all -i t1_SPGR.nii -s subjectname -all > Then use dt_rcon -s subjectname ... > > On 9/12/2024 7:45 AM, Ramesh Babu wrote: > > External Email - Use Caution > Dear All, > > I am new to dti analysis. I am trying analysis in a single subject. I set > the environment as

[Freesurfer] Error in dt_recon

External Email - Use Caution Dear All, I am new to dti analysis. I am trying analysis in a single subject. I set the environment as mentioned below. export DTI_DATA=export DTI_DATA=/mnt/data_analysis/mchp_projects/sneha/dti_analysis/FS_DTI_analysis export SUBJECTS_DIR=$DTI_DATA/su

[Freesurfer] Freeview issue

External Email - Use Caution Dear Expert, Recently I installed the latest version of freesurfer in Ubuntu OS 22LTS.. Freesurfer is installed successfully, but freeview gives some errors which I pasted below. Please provide your suggestions. Thank You Ramesh freeview This applicat

[Freesurfer] Freesurfer installation issue

External Email - Use Caution Dear Expert, I am trying to install Freesurfer-7.2 .deb package. I had this package earlier, and after formatting my system now, I am trying to install Freesurfer again. But I am facing the following issues. 'freesurfer_7.2.0_amd64.deb' is not a Debia

Re: [Freesurfer] 2mm thick image for hippocampal segmentation.

/6/2021 8:10 AM, Ramesh Babu wrote: > > External Email - Use Caution > Dear Eugenio and Philipp, > > Thank you very much for your suggestions. Could you please give more input > on "acquire the T1WI double and average it after coregistration, this > increases the

Re: [Freesurfer] 2mm thick image for hippocampal segmentation.

ses the SNR. > > - Generally, isometric resolutions are good due to the symmetry, of course. > > - Also on 1.5 T, you may go bit below 1 mm with good head immobilization, > and a longer scanning time. BRAVO in general is a good T1 option. > > > > Best, > > Philipp >

Re: [Freesurfer] 2mm thick image for hippocampal segmentation.

External Email - Use Caution Dear experts, Sorry for reposting. I am expecting some response from experts, so that I can proceed with confidence. For our project work, we are looking for hippocampal and its subfield volumes. Using GE 1.5T scanner, we tried a 3D BRAVO sequence with

[Freesurfer] 2mm thick image for hippocampal segmentation.

External Email - Use Caution Dear Experts, For our project work, we particularly looking for hippocampal and its subfield volumes. Using GE 1.5T scanner, we tried a 3D BRAVO sequence with 1x1x1 resolution, 256x256x160 dimension with 8* flip angle which produced images with a lot o

[Freesurfer] Flip image (resize)

External Email - Use Caution Dear Experts, The fMRI data, when viewed in SPM, some images have 3x3x4 voxel dimensions and some images have -3x3x4. Should I flip the image (using resize option) so that all images will have the same dimensions? or Should I leave it without flipping?

Re: [Freesurfer] Using subject specific template, atlas, & TPM

iki and see if you can make it work, and let us knof i > you have any issues. There are also surface-based atlases, but I suspect > thos are a lot less likely to be biased by brain shape (since we map to a > sphere anyway) > > cheers > Bruce > On Fri, 12 Jan 2018, Ramesh Babu

Re: [Freesurfer] Using subject specific template, atlas, & TPM

n > format as they need information not contained in most standard images, so > it won't be easy to get it into that format unless you use our training > utility (mri_ca_train) > > cheers > Bruce > > On Thu, 11 Jan 2018, Ramesh Babu wrote: > > Dear experts, >>

[Freesurfer] Using subject specific template, atlas, & TPM

Dear experts, I have analysed T1 data using Freesurfer. Now we have created atlas, template & tissue probability map using different methods and softwares. I need your help to use template in freesufer, so that we can compare with default template and our template. Please help me to put these imag

Re: [Freesurfer] non-brain region

- > > Emma Boyd > > Research Technician II > > Laboratory for Computational Neuroimaging > > Martinos Center for Biomedical Imaging > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu>

Re: [Freesurfer] Merging two groups

Dear Bruce, Thank you. Now its working fine. On Thu, Nov 30, 2017 at 3:46 PM, Ramesh Babu wrote: > Dear Bruce, > Thank you very much for reply. > > I have to link fsavarage also. Because recently I have formated my system, > the link between freesurfer and fsaverage is b

Re: [Freesurfer] Merging two groups

end > > then all your subjects will be listed in dir2 > > that should do the trick > > On Wed, 29 Nov 2017, Ramesh Babu wrote: > > Dear Bruce, >> >> Thank for your reply. I am getting confusion in creating symlink. >> ln -s /usr/local/freesurfer/subjects/fs

Re: [Freesurfer] Merging two groups

how to create symbolic link? Thank you Ramesh On Tue, Nov 28, 2017 at 8:27 PM, Bruce Fischl wrote: > Hi Ramesh > > probably easiest to symlink them > > cheers > Bruce > > On Tue, 28 Nov 2017, Ramesh Babu wrote: > > Hi, I have done recon-all -all processing for 2

Re: [Freesurfer] Merging two groups

re the copy is ok, then delete > the old version. rsync is good for this kind of thing too > > > On 11/27/2017 12:14 PM, Ramesh Babu wrote: > > Hi, > > I have done recon-all -all processing for 2 groups in separate > > subjects directories. I want to put all subjects in

[Freesurfer] Merging two groups

Hi, I have done recon-all -all processing for 2 groups in separate subjects directories. I want to put all subjects in one dkirectory. Should I copy paste all subject’s folders in one directory or is there any others steps to merge? Thanks in advance RB

[Freesurfer] Merging two groups

Hi, I have done recon-all -all processing for 2 groups in separate subjects directories. I want to put all subjects in one dkirectory. Should I copy paste all subject’s folders in one directory or is there any others steps to merge? Thanks in advance RB

Re: [Freesurfer] Changing operating system.

uld rerun a couple and see if things > change. > > cheers > Bruce > > > On Sat, 11 Nov 2017, Ramesh Babu wrote: > > Dear Experts, >> >> Recently I am facing lot of problem with Ubuntu OS 16lts. In one year I >> have formatted 4 times >> because o

[Freesurfer] Changing operating system.

Dear Experts, Recently I am facing lot of problem with Ubuntu OS 16lts. In one year I have formatted 4 times because of nvidia graphic card driver issue (happens after update) or some unknown reason ( I am not tech tech guy to figure out all the problem). Yesterday onwards problem started again. I

[Freesurfer] Selecting OS for image analysis

Dear Experts, I have purchased a new pc. I want to use for MRI and EEG analysis by using MATLAB, FSL, SPM, Fresurfer etc,. Which OS is suitable to handle these software? I have NVIDIA graphics card 610 in my system. I am using Ubuntu in another systm and little bit of experience in cent os. Than

Re: [Freesurfer] error report - talairach.m3z not found

Thank you Bruce On Thu, Jun 22, 2017 at 12:45 AM, Bruce Fischl wrote: > sounds like more in the graphics card, or just reduce the number of > simultaneous jobs > > On Wed, 21 Jun 2017, Ramesh Babu wrote: > > Dear Douglas Greve and Bruce, >> >> Thanks for your re

Re: [Freesurfer] error report - talairach.m3z not found

gt; > > looks like you need more memory in your gpu > > > > On 6/20/17 7:30 AM, Ramesh Babu wrote: > > Dear Expert, > > > > The recon-all -all process has stopped abruptly and error report shows > > that "cannot find or read transforms/talairac

[Freesurfer] error report - talairach.m3z not found

Dear Expert, The recon-all -all process has stopped abruptly and error report shows that "cannot find or read transforms/talairach.m3z". Please see the attached file. Processing was running in 5 terminal simultaneously and it has happened for two processing. Others exited without error. Could plea

Re: [Freesurfer] recon-all -all error end abruptly

gt; cheers > Bruce > On Tue, 6 Jun 2017, Ramesh Babu wrote: > > Dear Bruce, >> >> Today I ran the image processing on the same image which was stopped >> abruptly earlier. Now it is finished without any error. Please see the >> attached file before and after e

Re: [Freesurfer] recon-all -all error end abruptly

; > cheers > Bruce > On Mon, 5 Jun 2017, Ramesh Babu wrote: > > Dear Bruce, >> >> Please see the attached file which was completed normally. Earlier I have >> done this with 6 images simultaneously without any problem. But yesterday >> out of 6 image processin

Re: [Freesurfer] recon-all error

Dear Maria, I am also faced the similar problem when I used Philips DICOM. Then I converted to nifti format by using dcm2nii tool. It is working fine. You can also try. Best Ramesh On Mon, Jun 5, 2017 at 7:56 PM, Maria Economou wrote: > Dear FreeSurfer developers, > > Sorry for cross-posting,

Re: [Freesurfer] recon-all -all error end abruptly

eers > Bruce > On Mon, 5 Jun 2017, Ramesh Babu wrote: > > > Dear Expert, > > > > recon-all -all process for one subject end abruptly. I have attached the > > error report file. Please provide me some solution. > > > > > > Thanks > > Ramesh

[Freesurfer] recon-all -all error end abruptly

Dear Expert, recon-all -all process for one subject end abruptly. I have attached the error report file. Please provide me some solution. Thanks Ramesh Sun Jun 4 21:09:32 IST 2017 /mnt/research/freesurfer_analysis/subjects/grp127 /usr/local/freesurfer/bin/recon-all -all -i grp127_t1.nii -s grp1

Re: [Freesurfer] cuda-gpu problem

st end card of the 600 series. Unless you have a higher end Nvidia > card, such as the 970, 980, 1060 (or higher) your CPU will very likely be > faster in the recon-all process. > > Best, > > Peter > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.

Re: [Freesurfer] Installing and enabling cuda

/libcudart.so.4.2.9 As far as I know, freesurfer supports cuda-5 and it requires libcudart.so-5.0. That's why I have installed cuda-5. How did you enable freesurfer with cuda-8? Thanks Ramesh On Thu, May 25, 2017 at 5:42 AM, R Edgar wrote: > On 24 May 2017 at 00:36, Ramesh Babu wrote: &

Re: [Freesurfer] cuda-gpu problem

, 2017 at 3:37 PM, R Edgar wrote: > On 23 May 2017 at 01:10, Ramesh Babu wrote: > > > I have one question. When use -use-gpu flag, can I use -itkthreads 8 or > -use > > openmp 8 flag? > > That's not something I've tested. I think that OpenMP at least is OK > (t

Re: [Freesurfer] Installing and enabling cuda

amesh On Tue, May 23, 2017 at 3:38 PM, R Edgar wrote: > On 23 May 2017 at 01:13, Ramesh Babu wrote: > > > Ok. I will try cuda 8.0 and let you know the result. Should I install > cuda 5 > > before installing cuda 8? or Can I run both? > > You'll only be able to ha

Re: [Freesurfer] Installing and enabling cuda

Dear Richard, Ok. I will try cuda 8.0 and let you know the result. Should I install cuda 5 before installing cuda 8? or Can I run both? Thanks Ramesh On Tue, May 23, 2017 at 1:54 AM, R Edgar wrote: > On 22 May 2017 at 08:44, Ramesh Babu wrote: > > > After compiling in the same

Re: [Freesurfer] cuda-gpu problem

e not similar. Thank you for your feedback. I have one question. When use -use-gpu flag, can I use -itkthreads 8 or -use openmp 8 flag? Thanks Ramesh On Tue, May 23, 2017 at 1:51 AM, R Edgar wrote: > On 22 May 2017 at 07:39, Ramesh Babu wrote: > > > The following last line get

Re: [Freesurfer] Installing and enabling cuda

your help to check whether cuda is connected with freesurfer. How to check this. Thanks Ramesh On Mon, May 22, 2017 at 2:51 PM, R Edgar wrote: > On 21 May 2017 at 23:40, Ramesh Babu wrote: > > > Thank you for your reply. I tried to compile by looking FAQ about CUDA in > > Ubuntu

Re: [Freesurfer] cuda-gpu problem

utput) On Mon, May 22, 2017 at 2:55 PM, R Edgar wrote: > On 22 May 2017 at 03:10, Ramesh Babu wrote: > > > I have attached two documents. One document contains report with -use-gpu > > flag which I have interrupted and another document is without -use-gpu > flag, > > co

Re: [Freesurfer] Installing and enabling cuda

Edgar wrote: > On 16 May 2017 at 23:10, Ramesh Babu wrote: > > > I have come across that I have freesurfer support cuda version 5, but I > have > > already installed latest version. > > Can I use latest version for freeesurfer or should I install version 5? > > Si

[Freesurfer] Installing and enabling cuda

Dear Expert, I have come across that I have freesurfer support cuda version 5, but I have already installed latest version. Can I use latest version for freeesurfer or should I install version 5? Since I am not expert in this field I need guidance to remove latest version of cuda and installing an

Re: [Freesurfer] Hippo-subfiled Need Help

> > Cheers, > > /Eugenio > > > Juan Eugenio Iglesias > > Translational Imaging Group > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > -- > *From:* freesurfer-boun...@nm

Re: [Freesurfer] Need help to run freesurfer

/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/share/fsl/5.0 pc@RB:~$ Thanks RB On Sat, Apr 22, 2017 at 9:50 AM, Ramesh Babu wrote: > Dear ZK, > > I have done md5sum check.

Re: [Freesurfer] Need help to run freesurfer

582bddec653a4' which > you can get by typing: > >md5sum freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz > > > On 04/20/2017 08:04 AM, Ramesh Babu wrote: > > Dear Experts, > > > > I have installed in /usr/local/freesurfer. I am trying to follow t

[Freesurfer] Need help to run freesurfer

Dear Experts, I have installed in /usr/local/freesurfer. I am trying to follow the command given in the freesurfer web page. $> export FREESURFER_HOME=/usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.sh But I could not figure out the .sh file in the freesurfer folder. Please see

Re: [Freesurfer] New to freesurfer Needhelp to install in Ubuntu 16 lts

tell us what shell you are running. > > cheers > Bruce > On Fri, 14 Apr 2017, Ramesh > Babu wrote: > > > Dear Expert, > > > > I am new member of this freesurfer mailing list. I just downloaded > > freesurfer package and installed in /usr/local/frees

[Freesurfer] New to freesurfer Needhelp to install in Ubuntu 16 lts

Dear Expert, I am new member of this freesurfer mailing list. I just downloaded freesurfer package and installed in /usr/local/freesurfer. I am trying to follow the command given in the freesurfer web page. $> export FREESURFER_HOME=/usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfe