[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] mri_mcsim for individual subjects and references {Disarmed}

Hi Doug, Thanks for that! with regards to your last point Unfortunately, it does not help much. Much was made of the bug that Eklund, et al, found in the alphasim program (the AFNI mc simulator), but even after fixing it, the volume-based analyses still had very high false positive rates. This

[Freesurfer] long_stats results for group analysis

Hi I run the commands listed below and I was wondering if there is a way to get the average pc1 for each group. I get an average for the entire sample. What should I use instead of --osgm? long_stats_slopes --qdec ./qdec/long.qdec.table.dat --stats aseg.stats --meas volume --sd

Re: [Freesurfer] Number of subjects in data table

Yes, I used Windows to convert initially then also tried it over Libre Office. Ben On Tue, May 16, 2017 at 3:09 PM, Douglas Greve wrote: > that file has a bunch of carriage returns instead of new lines (obscure > unix vs windows problems). Did you convert the csv

Re: [Freesurfer] Number of subjects in data table

that file has a bunch of carriage returns instead of new lines (obscure unix vs windows problems). Did you convert the csv under windows? On 5/16/17 3:53 PM, Benjamin Ubani wrote: Hello Douglas, Sorry for the delay. I converted this file from a .csv format in order to keep the column format

Re: [Freesurfer] CA1 subfield extraction

Hi Stephanos, The easiest way is to extract label 206 (CA1) from [lr]h.hippoSfLabels-T1.v10.FSvoxelSpace.mgz using mri_extract.label, and then apply the resulting mask on the original (orig.mgz) or normalized (norm.mgz) volumes. From the subject’s mri directory: mri_extract_label

[Freesurfer] Importing external statistical map and overlaying over freesurfer anatomical

Hi Freesurfer list, I have a statistical map (.nii format) produced from analysis performed in BrainVoyager that I'd like to register with the anatomical model produced with Freesurfer's recon-all, this is on a single-subject basis from the same raw data. I have several questions with respect

Re: [Freesurfer] GLM_Fit Question

not sure what you're talking about On 5/16/17 2:55 PM, Mikael Novén wrote: Dear Freesurfer experts, I also have this problem and can’t seem to find the script. Would it be possible to get access to it? Thank you in advance, Mikael Novén ___

[Freesurfer] CA1 subfield extraction

Hello Freesurfer Developers, I want to perform texture analysis on the CA1 subfield of the hippocampus. Thus, I am using the recon-all command to generate the subfields. However, I want to perform texture analysis on the CA1 subfield only and I need to extract it from the original T1 image...

Re: [Freesurfer] decimate overlay

Hi Douglas, Thanks, that worked. However, for future reference, if it's necessary to keep the original values then put --no-rev Thanks Dorothy On Tue, May 16, 2017 at 10:31 AM, Douglas Greve wrote: > Try something like > > mris_apply_reg --src overlay4k.mgh --trg

Re: [Freesurfer] GLM_Fit Question

Dear Freesurfer experts, I also have this problem and can't seem to find the script. Would it be possible to get access to it? Thank you in advance, Mikael Novén ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] LME : longitudinal correlations between imaging and cognition scores

Hi Martin, Thank you for this detailed answer. Are replacing time by score or include score as time-varying covariate leading to the same result because of looking at the same effect ? My willing would be to find patterns of atrophy rate/progression correlated with cognitive score. In context

Re: [Freesurfer] problem in extract subcortical volume as ROI

try this https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat On 5/16/17 12:34 PM, Cong wrote: > Dear Doug > I think my problem may caused by that extracted ROI have different > coordination to original > T1 image, although they match well in freeview. For example, one voxel is >

Re: [Freesurfer] R: Thalamic seeds in FS-FAST

No, not yet On 5/16/17 1:10 PM, std...@virgilio.it wrote: Please I wonder whether the thalamic seeds from 8001-8014 are available in FS 6.0 and, specifically for FS-FAST for functional connectivity? Thanks. Regards, Stefano

Re: [Freesurfer] decimate overlay

Try something like mris_apply_reg --src overlay4k.mgh --trg overlay1k.mgh --streg surf4k surf1k On 5/16/17 12:41 PM, Dorothy Sincasto wrote: Hi Douglas, I am using the cortical surface for MEG time series reconstruction. I need to know which vertices belong to a specific area, i.e.

[Freesurfer] R: Thalamic seeds in FS-FAST

Please I wonder whether the thalamic seeds from 8001-8014 are available in FS 6.0 and, specifically for FS-FAST for functional connectivity?Thanks.Regards,Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] R: Thalamic seeds in FS-FAST

Please I wonder whether the thalamic seeds from 8001-8014 are available in FS 6.0 and, specifically for FS-FAST for functional connectivity?Thanks.Regards,Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Thalamic seeds in FS-FAST

The thalamic seeds from 8001-8014 are available in FS 6.0 and, specifically for FS-FAST for functional connectivity.Thanks.Regards,Stefano___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] CA1 subfield extraction

Hello Freesurfer Developers, I want to perform texture analysis on the CA1 subfield of the hippocampus. Thus, I am using the recon-all command to generate the subfields. However, I want to perform texture analysis on the CA1 subfield only and I need to extract it from the original T1 image...

[Freesurfer] R: Re: R: Re: selxavg3-sess error

Rerunning it is ok Messaggio originale Da: "Douglas Greve" Data: 16-mag-2017 18.21 A: Ogg: Re: [Freesurfer] R: Re: selxavg3-sess error Does this file exist ?

Re: [Freesurfer] (no subject)

just erode it once using mri_morphology, then subtract it from the un-eroded volume On Tue, 16 May 2017, Gamaliz wrote: Bruce,  I tried mris_fill, but it gives me a filled white matter volume (I already have that in the mri directory. I need the contour only.  Douglas, Looking into the --help

Re: [Freesurfer] decimate overlay

Hi Douglas, I am using the cortical surface for MEG time series reconstruction. I need to know which vertices belong to a specific area, i.e. vertices that belong to the PCC, AG... I got the surfaces from the HCP which has 4.002 vertices in each subject, then I decimated with mris_decimate 0.25,

Re: [Freesurfer] problem in extract subcortical volume as ROI

Dear Doug I think my problem may caused by that extracted ROI have different coordination to original T1 image, although they match well in freeview. For example, one voxel is [148,144,131] in extracted left thalamus but [71,130,89] in original T1.nii and T1.mgz. So how to extract a ROI

[Freesurfer] R: Re: R: Re: selxavg3-sess error

Yes, the file exists.Additionally, please take in account that I have run other FC analysis on this subj using other seed as ROI. Messaggio originale Da: "Douglas Greve" Data: 16-mag-2017 18.21 A: Ogg: Re: [Freesurfer]

Re: [Freesurfer] Freesurfer white matter outer edge to volume

Try visualizing it in freeview instead of fslview. On 5/16/17 12:11 PM, Gamaliz wrote: Bruce, I tried mris_fill, but it gives me a filled white matter volume (I already have that in the mri directory. I need the contour only. Douglas, Looking into the --help gave me a few ideas. I think the

Re: [Freesurfer] R: Re: selxavg3-sess error

Does this file exist ? /Applications/freesurfer/subjects/fMRI/subj067_GROUP/001/masks/brain.e3.nii.gz You can try deleting the /Applications/freesurfer/subjects/fMRI/subj067_GROUP/001/masks folder and re-running. On 5/16/17 11:53 AM, std...@virgilio.it wrote: selxavg3-sess -s

Re: [Freesurfer] Freesurfer white matter outer edge to volume

Bruce, I tried mris_fill, but it gives me a filled white matter volume (I already have that in the mri directory. I need the contour only. Douglas, Looking into the --help gave me a few ideas. I think the help page (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol ) should include this

[Freesurfer] (no subject)

Bruce, I tried mris_fill, but it gives me a filled white matter volume (I already have that in the mri directory. I need the contour only. Douglas, Looking into the --help gave me a few ideas. I think the help page (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol ) should include this

[Freesurfer] R: Re: selxavg3-sess error

selxavg3-sess -s subj067_GROUP -a fc.lamgseed.surf.lh -debugset echo = 1 ;breakswbreaksw endendwhile ( $#argv != 0 )while ( 0 != 0 )goto parse_args_return ;goto parse_args_return foreach grp ( $grpdefs )foreach grp ( ) goto check_params ;goto check_params if ( $#SessList == 0 ) thenif ( 1 == 0 )

Re: [Freesurfer] Volume comparison between groups and QDEC

On 5/11/17 3:25 PM, John Anderson wrote: Hi Doug, Why Qdec offer "volume, area, thickness ,...etc " in the drop down menu "measures"? In this menu there are many measures and I understand that I can run surface based analysis depending on the choice of this drop down menu. Is this

Re: [Freesurfer] Volumen for Aparc+aseg region 2 and 41

We do not report those regions because the volume-based approach (counting up voxels labeled 2 and 41) is less accurate than the surface-based approach (this is the CorticalWhiteMatterVol). On 5/15/17 1:10 PM, Gamaliz wrote: Regions 2 and 41 are labeled as Left-Cerebral-White-Matter

Re: [Freesurfer] Maps showing correlations between structural measures

You can do FDR or you can co cluster correction, but you can't do both. It looks like that paper only did FDR. If you want to do FDR, you can use mri_fdr. Run with --help for more info On 5/15/17 12:33 PM, Martin Juneja wrote: Thanks Dr. Greve. Regarding 2nd question, I am not sure how

Re: [Freesurfer] Contrast matrix for PVR

The 2nd is the correct matrix On 5/15/17 12:36 PM, Sahil Bajaj wrote: Hi everyone, From FreeSurfer manual and discussion forum, I found that volume and LGI can be correlated using mri_glmfit command with -pvr flag. For that, my fsgd file has age, gender as covariates and the file is as

Re: [Freesurfer] problem in extract subcortical volume as ROI

no idea. you'll proably have to contact the MRIcro group On 5/16/17 8:28 AM, Cong wrote: Dear FSers I extracted left thalamus as ROI volume from aseg.mgz by this command: / mri_binarize --i control001/mri/aseg.mgz --match 10 --o control001/roi/l_thal.nii/ I overlaid l_thal.nii to

Re: [Freesurfer] selxavg3-sess error

not sure what is going on. Is the script stem2fname in your path? If so, run selxavg3-sess with -debug as the first option and send the terminal output On 5/16/17 3:08 AM, std...@virgilio.it wrote: Hi list, this error occurs during selxavg3-sess in FS-FAST fcMRI meanval --i stem2fname stem

Re: [Freesurfer] mri_mcsim for individual subjects and references {Disarmed}

you can't really do permutation at the first level because the temporal autocorrelation and non-orthogonal design matrix violate the permutation assumptions. On 5/15/17 11:23 PM, Kevin Aquino wrote: Actually, would would be preferable would be running a permutations test something that you

Re: [Freesurfer] mri_mcsim for individual subjects and references {Disarmed}

On 5/15/17 10:34 PM, Kevin Aquino wrote: Hi all, First of all, Freesurfer V6 is working like a dream, my 0.7 mm segmentations are running really well and in comparisons to hi-resrecon in 5.3 and early beta, I'm having to do fewer manual corrections! Now for my questions, 1. I'm running

Re: [Freesurfer] Freesurfer white matter outer edge to volume

If you run it with --help, it will print out examples. Did you try that? On 5/16/17 9:26 AM, Bruce Fischl wrote: Hi gAbE you could try using mris_fill, or even mris_compute_volume_fractions cheers Bruce On Mon, 15 May 2017, Gamaliz wrote: My idea is to convert the registered white surface

[Freesurfer] perirhinal volumes

Dear Freesurfer experts, I would like to obtain perirhinal cortex volumes from structural images that have undergone recon-all. I see that the label subfolder contains left and right perirhinal cortex labels but the stats file does not. So a first step seems to be "converting" the label to

Re: [Freesurfer] probability maps

thanks Doug! I will give this a shot! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Mon, May 15, 2017 at 9:56 PM, Douglas Greve wrote: > you can do something like > > a = MRIread('map1.mgz'); > > b =

Re: [Freesurfer] Freesurfer white matter outer edge to volume

Hi gAbE you could try using mris_fill, or even mris_compute_volume_fractions cheers Bruce On Mon, 15 May 2017, Gamaliz wrote: My idea is to convert the registered white surface into a volume, so it can be shown in a volume viewer (not a surface viewer). I need to display a DTI image and

[Freesurfer] problem in extract subcortical volume as ROI

Dear FSers I extracted left thalamus as ROI volume from aseg.mgz by this command: mri_binarize --i control001/mri/aseg.mgz --match 10 --o control001/roi/l_thal.nii I overlaid l_thal.nii to control001.nii in MRIcro software in a Macbook and it looks well. However, when I

Re: [Freesurfer] LME : longitudinal correlations between imaging and cognition scores

Hi Matthieu, one option is to replace time with score in the model. That should be straight forward. The other option is to include score as a time-varying covariate. If your score is not varying much across time and you are more interested if the average score (or baseline score) affects

Re: [Freesurfer] 2 stage model longitudinal data analysis

There is usually three different approaches to analyze longitudinal data (and yours is longitudinal as you have 2 time points and are interested in change). - linear mixed effects models (matlab), recommended - 2 stage approach (long_mris_slopes), old approach, and superseded by LME. Can be

[Freesurfer] selxavg3-sess error

Hi list, this error occurs during selxavg3-sess in FS-FAST fcMRI meanval --i stem2fname stem Looks for stem.fmt where fmt is mgh mgz nii nii.gz bhdr img w, then returns stem.fmt. See also stem2fmt, fname2stem The file needs to exist on disk. --m 001/masks/brain.e3.nii.gz --o