[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

[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

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

[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

[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

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

ubjects. > Read the help and wiki 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 &g

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

segmentation tools use their own > 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: &

[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

Re: [Freesurfer] non-brain region

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

Re: [Freesurfer] Merging two groups

Dear Bruce, Thank you. Now its working fine. On Thu, Nov 30, 2017 at 3:46 PM, Ramesh Babu <mgrameshbabu2...@gmail.com> 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 fre

Re: [Freesurfer] Merging two groups

$subjects1) > ln -s $dir1/$s > 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. >&g

Re: [Freesurfer] Merging two groups

how to create symbolic link? Thank you Ramesh On Tue, Nov 28, 2017 at 8:27 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Ramesh > > probably easiest to symlink them > > cheers > Bruce > > On Tue, 28 Nov 2017, Ramesh Babu wrote: > > Hi, I have done re

Re: [Freesurfer] Merging two groups

s, I would copy them, make sure 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.

[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.

hat is too much of a burden you could 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 form

[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.

[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.

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

Thank you Bruce On Thu, Jun 22, 2017 at 12:45 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> 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, >

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

status 134 > > > > 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 r

[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

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

g else was running at the same time > > 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 >> at

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

ee if it completes? > > > 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 >&g

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,

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

have enough memory > > cheers > 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 prov

[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

Re: [Freesurfer] cuda-gpu problem

@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Ramesh Babu [ > mgrameshbabu2...@gmail.com] > *Sent:* Wednesday, May 24, 2017 3:51 AM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] cuda-gpu problem > > Dear Richard, > This command rec

Re: [Freesurfer] Installing and enabling cuda

.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 <freesurfer@gmail.com> wrote: > On 24 May 2017 at 00:36,

Re: [Freesurfer] cuda-gpu problem

, 2017 at 3:37 PM, R Edgar <freesurfer@gmail.com> wrote: > On 23 May 2017 at 01:10, Ramesh Babu <mgrameshbabu2...@gmail.com> wrote: > > > I have one question. When use -use-gpu flag, can I use -itkthreads 8 or > -use > > openmp 8 flag? > > That's not som

Re: [Freesurfer] Installing and enabling cuda

On Tue, May 23, 2017 at 3:38 PM, R Edgar <freesurfer@gmail.com> wrote: > On 23 May 2017 at 01:13, Ramesh Babu <mgrameshbabu2...@gmail.com> wrote: > > > Ok. I will try cuda 8.0 and let you know the result. Should I install > cuda 5 > > before installing cuda 8? o

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 <freesurfer@gmail.com> wrote: > On 22 May 2017 at 08:44, Ramesh Babu <mgrameshbabu2.

Re: [Freesurfer] cuda-gpu problem

are 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 <freesurfer@gmail.com> wrote: > On 22 May 2017 at 07:39, Ramesh Babu <mgrameshbabu2...@gmai

Re: [Freesurfer] Installing and enabling cuda

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 <freesurfer@gmail.com> wrote: > On 21 May 2017 at 23:40, Ramesh Babu <mgrameshbabu2...@gmail.com> wrote: > > > Thank you for your reply. I

Re: [Freesurfer] cuda-gpu problem

) On Mon, May 22, 2017 at 2:55 PM, R Edgar <freesurfer@gmail.com> wrote: > On 22 May 2017 at 03:10, Ramesh Babu <mgrameshbabu2...@gmail.com> wrote: > > > I have attached two documents. One document contains report with -use-gpu > > flag which I have interrupted

Re: [Freesurfer] Installing and enabling cuda

Edgar <freesurfer@gmail.com> wrote: > On 16 May 2017 at 23:10, Ramesh Babu <mgrameshbabu2...@gmail.com> wrote: > > > I have come across that I have freesurfer support cuda version 5, but I > have > > already installed latest version. > > Can I use lat

[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

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 <mgrameshbabu2...@gmail.com> wrote: > Dear ZK, > &

Re: [Freesurfer] Need help to run freesurfer

the tarball is 'd49e9dd61d6467f65b9582bddec653a4' 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/freesurf

[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

te: > Hi Ramesh > > you need to 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 an

[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