[Freesurfer] Quality of fMRI registration

Dear experts, When it comes to assessing the quality of fMRI integration in Freesurfer, is a value of > 0.5 considered a good registration? I was led to believe that from the multimodal tutorial website, and after checking the quality of my output I was satisfied with the result for each of

Re: [Freesurfer] Time Series to Surface

Use bbregister. Run with --help to get docs (make sure to use --projfrac 0.5). Once you have it on the surface, you can step through each frame in freeview On 04/05/2018 01:49 PM, Crawford, Anna wrote: > Hello, > > I have a time series (.hdr/.img) that I want to overlay onto a > surface,

Re: [Freesurfer] scan log generated by dcmunpack

> I am trying to unpack my DICOM folder and run recon-all. After dcmunpack, >> I selected 301 to run recon-all. But the recon-all didn't go through. >> Please see the attached scan.log, recon-all.log, error.log, and the pic >> of my DICOM folder. >> >> Thank yo

Re: [Freesurfer] scan log generated by dcmunpack

. > >Thank you so much. >Kan Din, MD >Assistant Professor- Department of Neurology and Neurotherapeutics >UT Southwestern Medical Center at Dallas >Tel: 214-648-9197 >Fax: 214-648-6320 > > > >UT Southwestern > > >Medical Center > >

Re: [Freesurfer] Longitudinal data from different sequences and scanners

All, Just wanted to follow up on this message. Does anyone have recommendations for the best way to compare this data longitudinally? Thanks very much, James On Thu, Mar 29, 2018 at 1:19 PM, James Gullickson wrote: > All, > > Our lab is working with longitudinal (two time

[Freesurfer] Time Series to Surface

Hello, I have a time series (.hdr/.img) that I want to overlay onto a surface, specifically the inflated surface from the anatomy. I suspect I have to use mri_vol2surf, which requires a source registration file. How do I get this file? Then once I have this file, will I be able to view step by

Re: [Freesurfer] scan log generated by dcmunpack

It looks like there is something wrong with that dicom file/series because the pixel spacing is "unknown". Where did the dicoms from from? Have they been anonymized? On 04/05/2018 12:12 PM, Kan Ding wrote: > Hello: > > I am trying to unpack my DICOM folder and run recon-all. After >

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

Those commands look ok. My suspicion goes to the use of --regheader. See whether the registration is ok with tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat On 04/05/2018 08:34 AM, srishti goel wrote: > Hi, > > I am trying to

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

can you email us the input file and the full command line you ran? On Thu, 5 Apr 2018, srishti goel wrote: So it gave this error: 3d normalization pass 1 of 2 white matter peak found at 110 HISTOalloc(-2147483648): could not allocate histogram Cannot allocate memory Best, Srishti

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

So it gave this error: 3d normalization pass 1 of 2 white matter peak found at 110 HISTOalloc(-2147483648): could not allocate histogram Cannot allocate memory Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

let's see if it works. If it does, you should be able to run recon-all -s SUBJID -make all cheers Bruce On Thu, 5 Apr 2018, srishti goel wrote: Should I re-run the recon-all after running the last command from recon-all.cmd? Best, Srishti Social/Clinical Research Specialist Child Imaging

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

Should I re-run the recon-all after running the last command from recon-all.cmd? Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Thu, Apr 5,

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

Hi Srishti if you look in the subject's scripts dir there should be a file named "recon-all.cmd". Try rerunning the last command in it (probably from the mri dir) cheers Bruce On Thu, 5 Apr 2018, srishti goel wrote: I am sorry, I am not sure what do you mean by running the command line

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

I am sorry, I am not sure what do you mean by running the command line directly? I use the following command: sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user srish...@email.unc.edu --wrap "export SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/; recon-all -s 13166

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

if you run the command that failed again on the command line directly (that is, not in recon-all) does it fail again? On Thu, 5 Apr 2018, srishti goel wrote: Hi Bruce, The machine definitely hasn't run out of memory. Here is the memory usage from recon-all.log                        total  

[Freesurfer] Qdec+Table format issue ?????

Dear Recipient, I am a Master student new comer in FS. I am trying toi use the QDEC ti analyse some longitudinal data. Most probably my issue is related with the file format. I tried to use several text editors (mac text editor, gedit and text wrangler) however I end up in 2 different errors

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

Hi Bruce, The machine definitely hasn't run out of memory. Here is the memory usage from recon-all.log total usedfree shared buff/cache available Mem: 26372696834330048 152102696 1294477294224 191963372 Swap: 2097148

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

Hi Srishti are you sure that your machine didn't just run out of memory? The recon-all.log file includes the amount of free (and total) memory at the time the process was started. cheers Bruce On Thu, 5 Apr 2018, srishti goel wrote: Hi, I have been trying to edit structural brains and

[Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

Hi, I have been trying to edit structural brains and very few times I would get the following error while running recon-all -s subjID white matter peak found at 110 cannot allocate memory Upon looking at the archive, there was only one similar issue and it was recommend to check mri_info as the

Re: [Freesurfer] query regarding creating an atlas from nifti volumes.

Hi Mageshwar gcs is a surface-based format for cortical segmentation. And it wouldn't be a conversion as much as it would be a training. If you can sample your regions onto the surface in .annot format you can use mris_ca_train to build a new gcs that you can then apply with mris_ca_label

Re: [Freesurfer] query regarding creating an atlas from nifti volumes.

Hi Mageshwar what kind of an atlas are you talking about? We have multiple atlases for different purposes. cheers Bruce On Thu, 5 Apr 2018, Mageshwar Selvakumar wrote: Dear All, I am a newbie to freesurfer and I would like to use our in-house built probabilistic atlas(each region as a

Re: [Freesurfer] error rerunning recon-all (exited with ERRORS)

Hi Anna from your log file it looks like some other process is using more than 2/3 of the memory on your machine: total used free sharedbuffers cached Mem: 24729588 1685252478770644095060 0 10543292 -/+ buffers/cache:6309232

[Freesurfer] Abstract submission deadline extended - 1st International Workshop on Predictive Processing

Hello Researchers, We have received request from lot of researchers to extend the deadline for abstract submission, We are happy to announce that the deadline for abstract submission for 1st International Workshop on Predictive Processing (WoPP) has been extended upto 16th April 2018.

[Freesurfer] mri_vol2surf: unable to compare volume maps

Hi, I am trying to compare my volume maps (negative_allsocial_proportion.nii) to someone else's (SN_like_cortical_lh.nii.gz) who have it on a surface (mni152_subject). So I used the steps for mri_vol2surf command as follows: Commands: mri_vol2surf --src negative_allsocial_proportion.nii

[Freesurfer] fmriprep to fsfast interface

Hello, I've been working on taking the outputs of the fmriprep BOLD preprocessing tool (https://fmriprep.readthedocs.io/en/latest/index.html) and coercing them into the fsfast structure so that first levels can be run with mkanalysis-sess and selxavg3b-sess. It's been a bit trickier than

[Freesurfer] query regarding creating an atlas from nifti volumes.

Dear All, I am a newbie to freesurfer and I would like to use our in-house built probabilistic atlas(each region as a binary mask and available as nifti files). I would like to create an atlas out of it and use it for our analysis. On searching the previous mailing list I came across a