[Freesurfer] mri_glmfit-sim running for 4 days and still not finished

External Email - Use Caution Dear freesurfer community, I have been working with the freesurfer stat files for some time now but never got to explore the group analysis pipeline. I tried this mri_glmfit command to see the correlation of my anatomical data(57 subjects) with a cli

[Freesurfer] MGN and LGN in ThalamicNuclei segmentation

External Email - Use Caution Hello, I'm interested in locating the MGN and LGN using segmentationThalamicNuclei, but there is a mismatch between their location in the discrete segmentation (ThalamicNuclei.v10.T1.mgz) and the underlying  probability maps obtained by setting envi

Re: [Freesurfer] Error recon-all mri_cc

Can you upload the subject so I can take a look? Instructions below From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log  into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "a

Re: [Freesurfer] mri_glmfit error

Can you send the full terminal output? On 6/15/2020 10:41 PM, 邓刊 wrote: External Email - Use Caution Hello Freesurfer Experts! I met the mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08.I am trying to run a 8 group 3 variables analysis: with diagnosis bei

Re: [Freesurfer] mri_glmfit-sim running for 4 days and still not finished

Can you send your command line and terminal output? ...not all of it if it has been running for 4 days:) On 6/16/2020 8:34 AM, Mageshwar Selvakumar wrote: External Email - Use Caution Dear freesurfer community, I have been working with the freesurfer stat files for some time now but

Re: [Freesurfer] Ventricular location

Try  mri_segcentroids. Run it with --help to get docs On 6/16/2020 8:39 AM, Ian wrote: External Email - Use Caution Hi Freesurfers. I'm looking to find the center of the various Ventricles.  Are they included in the freesurfer segmentation images with a specific code? If not, what

Re: [Freesurfer] MGN and LGN in ThalamicNuclei segmentation

Dear Julien, Thanks for your very interesting email! One thing at the time: At each voxel, the discrete segmentation is given by the label with the highest probability. Therefore, there is no fixed threshold. One voxel my require a probability of 0.51 to "win" (if another class has probability

Re: [Freesurfer] Longitudinal Stream Problem

I have your data, but it does not have the base image. Can you upload that as well? On 6/15/2020 5:15 PM, Danielian, Laura (NIH/NINDS) [E] wrote: External Email - Use Caution Hi Douglas, I just upload the files as danielian.tar.gz.  I didn’t notice any damage or artifact on this par

Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}

External Email - Use Caution Hi Bruce, I just used the load command. See below. >> load('rh.wang15_mplbl.mgz') Error using load Unknown text on line number 1 of ASCII file rh.wang15_mplbl.mgz +u�^[1]�". Cheers, Mason Mason T Wells, MSc PhD student School of Optometry and Visi

Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}

You can't just use the load() command. Try rh = MRIread(filename) The pixel data will be in rh.vol On 6/16/2020 10:25 AM, Mason Wells wrote: External Email - Use Caution Hi Bruce, I just used the load command. See below. >> load('rh.wang15_mplbl.mgz') Error using load Unknown text

Re: [Freesurfer] Ventricular location

Yes, I put a linux version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids On 6/16/2020 10:32 AM, Ian Hardingham wrote: External Email - Use Caution Is this only in FSL 7 Doug? I can't find it in 6. On 16/06/2020 14:59, Douglas N. Greve wrote: Try  mri_segcent

[Freesurfer] extracting clusters for each timepoints for longitudinal analyses

External Email - Use Caution Hello, I ran a pet longitudinal paired t-test analysis with 2 timepoints using mri_glmfit and I found significant clusters. I want to extract the values of these significant clusters for each timepoints. How do I go about doing this? Thank you. Best,

Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}

You need to use load_mgh or MRIread (which we distribute) Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Mason Wells Sent: Tuesday, June 16, 2020 10:26 AM To: Freesurfer support list Subject: Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}

Re: [Freesurfer] extracting clusters for each timepoints for longitudinal analyses

did you run the correction for multiple comparisons to get your clusters? If so, then there should be a table with a row for each subject and a column for each cluster. On 6/16/2020 11:03 AM, miracle ozzoude wrote: External Email - Use Caution Hello, I ran a pet longitudinal paired

Re: [Freesurfer] extracting clusters for each timepoints for longitudinal analyses

External Email - Use Caution Thanks Doug. I ran multiple comparisons to get the clusters. However, I want to extract the clusters values for the individual timepoints. The paired t-test does a paired-difference (timepoint1 - timepoint2) and I presume the significant clusters come

[Freesurfer] Ventricular location

External Email - Use Caution Hi Freesurfers. I'm looking to find the center of the various Ventricles.  Are they included in the freesurfer segmentation images with a specific code? If not, what approach would you use? Thanks, Ian -- *Ian Hardingham* __

Re: [Freesurfer] extracting clusters for each timepoints for longitudinal analyses

ok, still  pretty easy mri_segstats --seg ocn.mgh --exclude 0 --i timepoint1.mgh --avgwf timepoint1.table.dat where ocn.mgh is something like cache.th13.abs.sig.ocn.mgh timepoint1.mgh is the stack of timepoint 1 for all subjects The output will be a table with subjects on the rows and clusters

Re: [Freesurfer] extracting clusters for each timepoints for longitudinal analyses

External Email - Use Caution Lovely. Thank you very much Doug. I appreciate your help. Best, Paul On Tue, Jun 16, 2020 at 12:41 PM Douglas N. Greve wrote: > ok, still pretty easy > > mri_segstats --seg ocn.mgh --exclude 0 --i timepoint1.mgh --avgwf > timepoint1.table.dat > > w

Re: [Freesurfer] Longitudinal Stream Problem

External Email - Use Caution Hi Douglas, OK I just uploaded the base separately. danielianbase.tar.gz I thought it was part of the original bundle. Sorry! Laura From: "Douglas N. Greve" Reply-To: Freesurfer support list Date: Tuesday, June 16, 2020 at 10:10 AM To: "frees

Re: [Freesurfer] Ventricular location

External Email - Use Caution Is this only in FSL 7 Doug? I can't find it in 6. On 16/06/2020 14:59, Douglas N. Greve wrote: Try  mri_segcentroids. Run it with --help to get docs On 6/16/2020 8:39 AM, Ian wrote: External Email - Use Caution Hi Freesurfers. I'm looking

Re: [Freesurfer] Ventricular location

External Email - Use Caution Thank you so much Doug. Ian On 16/06/2020 15:44, Douglas N. Greve wrote: Yes, I put a linux version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids On 6/16/2020 10:32 AM, Ian Hardingham wrote: External Email - Use C

[Freesurfer] version 7 docker container

External Email - Use Caution Hello I was wondering if Freesurfer version 7 will be released as a container on docker hub? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesur

Re: [Freesurfer] MGN and LGN in ThalamicNuclei segmentation

External Email - Use Caution Thanks Juan. Nevermind. It turns out that I was comparing a discrete segmentation done with v10 (Freesurfer v6 or older) with posterior probability maps obtained using v12 (Freesurfer 7.0) in the same subject. The locations of the MGN and LGN segmen

[Freesurfer] freeview of freesurfer 7.1 incompatible with merged overlays

External Email - Use Caution Hello Freesurfer experts, I recently upgraded to Freesurfer 7.1. Many nice changes so thanks for that. I often work with merged gifti files and the previous stable version of Freesurfer/Freeview (6.0) had no issue with them. Now, Freeview can view m