Re: [Freesurfer] Missing files in mri_glm

> > > On Mon, Sep 24, 2018 at 12:36 PM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > > What version of FS are you using? The pcc may only be in the v6. > > On 09/24/2018 12:10 PM, srishti goel wrote: > > > >    

Re: [Freesurfer] if: missing file name

: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180919/ae9daaec/attachment-0001.rtf >> -- next part -- >> An embedded and charset-unspecified text was scrubbed... >> Name: ATT1.txt >> Url: >> http://mail.nmr

Re: [Freesurfer] mri_glmfit-sim error

Can you verify that the followign file exists, that you have read permission, and that you can successfully load it into freeview? /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white On 9/21/18 11:41 AM, C.P.E. Rollins wrote: External Email - Use Caution Hello

Re: [Freesurfer] make_average_subject error

Can you send the make_average-subject command and log file? On 9/21/18 7:03 AM, C.P.E. Rollins wrote: External Email - Use Caution Hello Freesurfer Developpers, I'm attempting to make a study specific template using all of my subjects as input using the make_average_subject command, but

Re: [Freesurfer] GLM

you need to have four classes, young-female, young-male, old-female, old-male On 9/21/18 3:15 AM, 郑凤莲 wrote: External Email - Use Caution Dear experts, I am using FS 6.0 for some studies. I want to calculate the thickness difference between males and females in two group, Young group

Re: [Freesurfer] calculated cortical thickness from segmented binary gray matter and white matter images from other software

Not by default with our software. You could create white and pial surfaces, but they would not be very accurate, and there would be no way to fit the surfaces to the segmentations. On 9/21/18 10:21 AM, yuanchao.zha...@gmail.com wrote: External Email -

Re: [Freesurfer] Clarification about .annot file format

Thanks Chris, can you point us to the offending wiki page? doug On 9/28/18 12:44 PM, Christopher Markiewicz wrote: External Email - Use Caution Hi all, I believe I've gotten to the bottom of this, and the problem is incorrect documentation, both in the read/write_annotation.m files

Re: [Freesurfer] Clarification about .annot file format

#Annotation Chris From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu> Sent: Friday, Sep

Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

Probably it was interrupted and the file as not completely written, or you ran out of space on the disk. If you start over, does it continue to happen? On 11/16/18 4:15 PM, Batuhan Erkat wrote: External Email - Use Caution Hello, I am using FreeSurfer solely for reconstruction. I am

Re: [Freesurfer] FSGD file

Class CMT Variables Age gender Input fs_VF HC 46 Female Input fs_RF HC 24 Female ... My group.diff.mtx should be: 1 -1 0 0 0 0 0 Is it ok? Thanks a lot Raffaele Il giorno gio 3 gen 2019 alle ore 20:11 Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> ha s

Re: [Freesurfer] using tkregister2 to check registration to custom atlas

Not sure what you are trying to do, but if you want to check the tal reg of a typical analysis, you can run tkregister2 --mov $SUBJECTS_DIR/fsaverage/mri/orig.mgz --targ $SUBJECTS_DIR/subject/mri/orig.mgz --ixfm $SUBJECTS_DIR/subject/mri/transforms/talairach.xfm -outxfm

Re: [Freesurfer] mni --> RAS T1

Hi Don, have you checked out this web page? http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 1/15/19 7:11 AM, Krieger, Donald N. wrote: External Email - Use Caution Is there a 4x4 transformation somewhere to convert mni coordinates to RAS T1 coordinates, I.e. something

Re: [Freesurfer] Talairach Transform failure

What do you mean that the tal volume does not load as a mov volume? Can you send the terminal output from tkregister2? On 1/16/19 10:01 AM, Daniel Ferreira wrote: External Email - Use Caution Dear Bruce, Martin, and experts, I posted an issue a few days ago. I have been looking

Re: [Freesurfer] preproc-sess mask issue

es, > Kevin > Date: Tue, 15 Jan 2019 21:47:37 + From: "Greve, Douglas N.,Ph.D." > Subject: Re: [Freesurfer] preproc-sess mask > issue To: "freesurfer@nmr.mgh.harvard.edu" > Message-ID: > <5b4ea669-5ade-6be4-2435-aed05faf1...@mgh.harvard.edu> Conten

Re: [Freesurfer] Large cluster size significant clusters

You can do the analysis in a particular region with masking (--mask input to mri_glmfit). You can also load the uncorrected overlay into freeview and adjust the threshold until you get  a cluster distribution you like, then use that threshold in mri_glmfit-sim On 1/16/19 4:44 PM, Azeez,

Re: [Freesurfer] Talairach Transform failure

terface {macro,mini,micro} > % >   Screen:  249 340 (28,28,28), inorm = 1, mov_frame = 0 >   Anat:    (124  85 127)   (   4.0   -1.0   43.0)  32.    27.7 >   Func:    (180 -142  42)   ( -52.4  -86.4  270.1) OutOfBounds > ---

Re: [Freesurfer] Talairach Transform failure

y black. How > should I continue from here? If the registration is so far off that it > is out > of the field of view, what should I do next? > > Thanks > > Dani > > El mié., 16 ene. 2019 a las 22:54, Greve, Douglas N.,Ph.D. > (mailto:dgr...@mgh.harvard.edu>>)

Re: [Freesurfer] convert surface-based label to volumetric space...mri_label2vol?

measurement applied at the single subject > level, and I was looking to generate and apply a single binary mask in > 3D space to all 100 schizophrenia patients' normalized functional > scans. Any suggestions? I appreciate your input. > > Cheers, > > Stephanie > >

Re: [Freesurfer] wm and vcsf nuisance regressors

Hi Mona, when you run fcseed-config you can specify to use -mean or -pca npca. -mean produces the mean waveform. -pca will run a PCA on all voxels and take the first npca components. In principle, using more components will fit more of the noise. But it can also make the design more poorly

Re: [Freesurfer] FSFAST poor registration

What version of FS are you using? version 6 initializes with mri_coreg (the FS equivalent of spm_coreg). On whole-brain data, I've found this to be very robust. Is your data whole-brain? On 1/18/19 5:10 AM, Keri Woods wrote: External Email - Use Caution Hi I have a problem very

Re: [Freesurfer] convert surface-based label to volumetric space...mri_label2vol?

There should already be two volumes (aparc+aseg.mgz and aparc.a2009s+aseg.mgz) which you can simply convert to nifti with mri_convert file.mgz file.nii.gz On 1/15/19 2:14 PM, Stephanie Hare wrote: > > External Email - Use Caution > > Good afternoon, > > I'm new to Freesurfer; my

Re: [Freesurfer] preproc-sess mask issue

Yea, the 5.3 stream used FSL brain masking to make the masks for the fmri. Version 6 uses the FS brain mask transferred into fmri space. Inevitably, you will have to do a lot of reprocessing. The simplest thing to do is to delete the mask files in session/bold/masks and sessoin/bold/RRR/masks

Re: [Freesurfer] Errors in white matter surfaces from scan collected on 3T Siemens Skyra scanner at .6 mm resolution

Not sure. Can you tar up the subject and send me the file here  ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming? Let me know when it is transferred. On 1/22/19 12:03 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > > External Email - Use Caution > > Hi, > > We collected an MP-RAGE scan

Re: [Freesurfer] Functional connectivty walkthrough step 8 error

Can you send the full terminal output and/or the log file? On 1/22/19 2:53 PM, Amrita Bedi wrote: > > External Email - Use Caution > > Hello Freesurfer developers, > > I was following the functional connectivity walkthrough for resting > stage BOLD data and I got the attached error when

Re: [Freesurfer] Version 6.1 and aseg histograms

On 1/22/19 2:59 PM, Hatton, Sean wrote: > External Email - Use Caution > > Hi all, > > Two quick questions: > > 1. Is there an expected timeframe for when FreeSurfer 6.1 (or next version) > is published? Not a firm date. We have started the process to release a new version. Last

Re: [Freesurfer] "slides" link is not working

try this one http://surfer.nmr.mgh.harvard.edu/pub/docs/GLM.pptx On 1/22/19 7:47 PM, Peters, Douglas G wrote: > > External Email - Use Caution > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples > > > Error Message: > > > Not Found > > The requested URL

Re: [Freesurfer] Error in running make_average_subject

Sorry, the disk that held that patch failed and we did not have a backup so not everything was restored. I just put this file there: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface Copy it to $FREESURFER_HOME/bin. Let me know how it goes On 12/10/18

Re: [Freesurfer] Command to convert subcortical values into subcortical segmentation

not sure that you are trying to do. An annot is usually used for cortical segmentation, not subcortical On 12/9/18 5:57 PM, Conchy PF wrote: External Email - Use Caution Hello FS experts, I was wondering if there is a command similar to annotval2surfoverlay.m that allows converting

Re: [Freesurfer] Power analysis

The gamma and gammavar files are vertex-wise values. You can load them in matlab with something like g = MRIread('gamma.mgh'); gv = MRIread('gammavar.mgz'); but you will need the vertex that you are interested in (or do for all vertices). You can use fast_glm_power.m in the FSFAST toolbox to

Re: [Freesurfer] glm analysis

That matrix will test for an effect of group regressing out the effect of age. I would first test for an interaction between group and age with 0 0 0 1 -1 0 0 0 0 1 0 -1 Assuming that there is no effect, then I would re-run with DOSS (different-offset, same-slope) with a contrast like 1 -1 0 0

Re: [Freesurfer] GLM multiple comparison correction

That is not normal. Are you sure you are looking at the different maps that are created? Also, we are recommending that people not use MCZ (especially with such a low threshold). Permutation is more accurate. See

Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices {Disarmed}

rvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, December 11, 2018 10:49 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices External Email. Use Caution. That all looks lik

Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices

That all looks like it would work to me. Another thing you can try is the way we create the wmparc.mgz using mri_aparc2aseg. You can find the commandline in the recon-all.log file (make sure to set the output name so that you don't overwrite wmparc.mgz). You can specify the max distance away

Re: [Freesurfer] Increasing the Number of a non-FreeSurfer Parcellation

can you include previous emails so that we know what you are talking about? On 12/11/18 7:15 AM, Maedeh Khalilian wrote: External Email - Use Caution Dear Bruce The parcellation I have is not on surface, it is volumetric. I wanna increase the number of its ROIs, I thought maybe I can

Re: [Freesurfer] R: LGI value aberrant high

Sorry, the lGI code is not being maintained anymore On 12/11/18 4:00 AM, Lorenzo Ferri wrote: External Email - Use Caution Dear expert I am trying to calculate LGI for a subject. Now with some of your suggestions it runs, but after one hour and half it gives me this errors

Re: [Freesurfer] fdr correction problem

do you mean that nothing survived threshold? That happens sometimes. On 12/10/18 8:03 AM, 1013364183 wrote: External Email - Use Caution Dear Bruce?? I have fdr correction for sig.mgh obtained by mri_glmfit, but the corrected graphs are all 0. Why is this, the instructions and the

Re: [Freesurfer] Robust PET signal projection

you can use mri_vol2surf to sample at different depths. If you want a simple average across cortex, then you can use --projfrac-avg .35 .65 .05 If you want to do more sophisticated weighting, then you will have to sample at each layer and then combine the files (eg, fscalc). Unless you have very

Re: [Freesurfer] Fwd: fcseedcor output

gt; Cc: dgr...@mgh.harvard.edu > Date: Sat, 08 Dec 2018 22:25:20 +0330 > Subject: Fwd: fcseedcor output > > > -Original Message- > From: "Sara Jafakesh" > To: "Greve, Douglas N.,Ph.D." > Date: Sat, 08 Dec 2018

Re: [Freesurfer] Fwd: fcseedcor output

ound. > How can I fix it and obtain connectivity matrix with fcseedcor? > thank you with your help , > sara > > -Original Message- > From: "Greve, Douglas N.,Ph.D." > To: Sara Jafakesh , > "freesurfer@nmr.mgh.harvard.edu" >

Re: [Freesurfer] Recon command with T1 and T2

Yes, include the -T2pial flag On 12/11/2018 12:06 PM, Maksimovskiy, Arkadiy wrote: > > Dear Experts, > > > I am planning to run "recon" using T1 and T2 images, and was wondering > if you wouldn't mind confirming whether this is the right command with > recon: > > > recon-all -s ${subject} -i

Re: [Freesurfer] Extracting both the GM and WM ROIs

what do you mean by the white matter region? The aparc only labels cortex, which is, of course, GM. If you mean the WM adjacent to the aparc, have you looked at the wmparc.mgz file? On 12/11/2018 05:16 PM, Song, Da-Yea wrote: > > External Email - Use Caution > > Hello, > > I’ve been

Re: [Freesurfer] Command to convert subcortical values into subcortical segmentation

use MRIRead & MRIWrite to change the values in aseg.mgz? How > can I do it? > > Thank you and best regards, > > Conchy > > On Tue, Dec 11, 2018 at 4:18 PM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > > not sure that you are trying to do.

Re: [Freesurfer] Conversion of registration files

Try lta_convert On 12/11/2018 03:46 PM, Jane Tseng wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > I was wondering if there is any way to convert the .dat file output > from spmregister (generated using Freesurfer version 5.3) to a .lta > file? Thank you! > >

Re: [Freesurfer] Power analysis

> approach to read them the same? > Thank you, > Laura > > > > >> El 11 dic 2018, a las 16:54, Greve, Douglas N.,Ph.D. >> escribió: >> >> The gamma and gammavar files are vertex-wise values. You can load them >> in matlab with something like >

Re: [Freesurfer] Error in running make_average_subject

null) > > Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:16:02 > UTC 2018 x86_64 x86_64 > x86_64 GNU/Linux > > Thanks > > Emanuel > > > On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>

Re: [Freesurfer] Extracting both the GM and WM ROIs

urfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas > N.,Ph.D. > Sent: Tuesday, December 11, 2018 5:42 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Extracting both the GM and WM ROIs > > what do you

Re: [Freesurfer] NormMean information

It could be anything related to the T1-weighting, so T1 itself or PD. It is possible for the T2* to affect it, but usually the echo time is too short for it to make much of a difference. I could imagine some other indirect effects because of the normalization itself. The normMean was not added

Re: [Freesurfer] Inferior colliculus and Brainstem-cochlear-nucleus

We don't have ways to automatically segment those (yet). They were optimistically added to the LUT a few years ago:) On 12/14/18 10:49 AM, Chama Belkhiria wrote: External Email - Use Caution Dear comittee, I need ROIs of Inferior Colliculus and Brainstem-cochlear-nucleus. Can

Re: [Freesurfer] How to use FIR to get HRF shape

The FIR resolution is set with the TER parameter (-TER for mkanalysis). You can try setting the TER to something shorter than the TR. This may or may not work depending upon your jittering (it would have been betterto have optseqed the stimuli with this in mind). On 12/13/2018 12:23 PM, Lauri

Re: [Freesurfer] mris preproc for folding index

tell me the difference between white.K and white.H > conceptually and mathematically? > > On Wed, Dec 19, 2018 at 2:27 PM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > > something like --meas white.K or white.H > > > On 12/19/2018 04:23 PM, M

Re: [Freesurfer] mris_fwhm problem

The smoothing works through iterative nearest neighbor smoothing, so the fwhm is essentially discretized because you can't have fractions of an iteration. It looks like fwhm=0.66 is closer to 0 iterations than 1 iteration, so it chooses 0. On 12/21/18 11:23 AM, sha...@nmr.mgh.harvard.edu

Re: [Freesurfer] mris_fwhm problem

No, not in the current framework. Even if there were, fwhm=.66 would not give you much smoothing. The intervertex distance is about 1mm, at fwhm=.66mm, the nearest vertex would be about 3 standard deviations away, meaning that the smoothing would be minimal. On 12/21/18 12:12 PM,

Re: [Freesurfer] ?????? ?????? ?????? Triangular mesh sampling problem

Yes, it can. You can also use mris_apply_reg, which is probably easier to use. Run it with --help to get more info On 11/29/2018 12:18 PM, 1013364183 wrote: > > ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution > > Dear Bruce, > ?0?2 ?0?2I want to know if mri_surf2surf can map high

Re: [Freesurfer] Beta extraction

Use something like mri_segstats --seg ocn.mgh --i beta.mgh --excludeid 0 --avgwf beta.clusters.dat See mri_glmfit-sim --help for more info on the OCN file and mri_segstats --help for info on the avgwf file On 11/29/2018 04:40 PM, Jahan, Bushra wrote: > I am wondering how to extract beta

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

Hi Matthieu, sorry for the delay On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote: > External Email - Use Caution > > Dear Freesurfer's experts, > > I tried to use PETSurfer to correct partial volume effect on my FDG PET > images, testing both Muller-Gartner and RBV corrections. > > I

Re: [Freesurfer] create ctab from annot

From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas > N.,Ph.D. > Sent: Monday, December 03, 2018 7:11 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [EXTERNAL] Re: [Freesurfer] create ctab from annot > >

Re: [Freesurfer] create ctab from annot

You can use mri_annotation2label to extract a color table from the annotation On 12/03/2018 07:06 PM, Bruce Fischl wrote: > Hi Stephanie > > can you give us some details about how you generated your fine-grained > parcellation? > > cheers > Bruce > On Mon, 3 Dec 2018, Winkelbeiner, Stephanie A

Re: [Freesurfer] fcseedcor output

hi sara, can you include the entire email chain so that I can see the context? On 12/7/18 4:19 PM, Sara Jafakesh wrote: External Email - Use Caution Dear Dr.GREVE , thank you for your reply my full terminal outpou is : [user@localhost subjects]$ fcseedcor -s subj1 -fsd rest -seed

Re: [Freesurfer] extracting the version of FreeSurfer used to process some data

look at subject/scripts/build-stamp.txt On 12/7/18 5:09 PM, David Groppe wrote: External Email - Use Caution Hi FreeSurfers, I'm working with some data that has been collected and processed with FreeSurfer over several years. Consequently, some individuals have been processed with

Re: [Freesurfer] fMRI time series extraction

On 12/06/2018 02:07 PM, Zhi Li wrote: > > External Email - Use Caution > > Thank you very much, Douglas. It works now. How could I know the ROI > index of each column in the .dat file? If you add --sum sum.dat, the sum file will tell you the order > And if it is available to use pca

Re: [Freesurfer] fMRI time series extraction

The easiest thing would be to run mri_segstats --annot subject lh  yourannot --excludeid 0 --i fmc.odd.sm5.fsaverage.lh.nii.gz --avgwf avgwf.dat avgwf.dat will have a row for each fmri time point and a column for each parcellation On 12/06/2018 01:45 PM, Zhi Li wrote: > > External

Re: [Freesurfer] How to run GLM FIT simulation in parallel?

gt; > I have 45 subjects as input. SLURM is also a parallel processing > pipeline similar to PBS, Grid Engine, or Condor: > https://en.wikipedia.org/wiki/Slurm_Workload_Manager > I am not sure how can I speed up the mri_glmfit-sim processing. > > Thanks ! > > On Thu, Dec 6,

Re: [Freesurfer] Fwd: Overall maxima is high and still no significant cluster

with --perm-force > > > Can you please tell me how can I fix this issue or if I can run with > --perm-force? > > > Thanks for the help. > > > On Thu, Dec 6, 2018 at 9:37 AM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > >

Re: [Freesurfer] How to use FIR to get HRF shape

Hi Lauri, what is non-ideal about it? doug On 12/06/2018 05:30 PM, Lauri Tuominen wrote: > External Email - Use Caution > > Hi there, > > I would like to know if a condition leads to a delayed HRF peaking. > > To device an experiment to answer this, I collected finger tapping pilot data

Re: [Freesurfer] Fwd: Overall maxima is high and still no significant cluster

For it to show up in the output file, the cluster-wise pvalue must be < .05 (CWT). To see all the clusters regardless of significance, run it with a CWT of 1. If you want to run with a more liberal cluster forming threshold (CFT), you can try using permutation. See

Re: [Freesurfer] mris_preproc paired diff outputs 0 values

If you just want to look at the difference maps, you can load the mris_preproc output stack as an overlay, then scroll through each one of them. You're still looking at each one of them, but you don't have to open them up one-by-one. On 12/05/2018 02:21 PM, Sims, Sara A wrote: > >

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

On 11/30/2018 07:15 AM, Matthieu Vanhoutte wrote: > > External Email - Use Caution > > Hi Douglas, > > Thank you for answering. Please find below new questions. > Bien cordialement, > > > Le ven. 30 nov. 2018 à 00:00, Greve, Douglas N.,Ph.D. > mailto

Re: [Freesurfer] Direction of significant group comparison

You can tell from the sign of the "VtxMax" column that indicates the maximum in the cluster. If you used a signed test (pos or neg), then they will all have the given sign. If  you used an unsigned test (abs), then they may have different signs. On 12/04/2018 11:54 AM, Backhausen, Lea wrote:

Re: [Freesurfer] Extracting ROI from atlases

You can use mri_binarize --i aparc+aseg.mgz --match 1028 --o ctx-lh-superiorfrontal.nii.gz See  $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use On 12/04/2018 12:51 PM, Song, Da-Yea wrote: > > External Email - Use Caution > > Hello, > > Is there a command to extract

Re: [Freesurfer] volume and mean intensity values from single nii file with multiple ROIs

Use mri_segstats. Run with --help to get more info On 12/03/2018 06:12 AM, Anik Dar wrote: > > External Email - Use Caution > > Dear All, > > I have segmented the midbrain of each subjects into different > subregions (peduncle, substantia nigra, red nucleus etc) using an > atlas. I am

Re: [Freesurfer] Longitudinal Stream - LONG step

Does the orig.mgz file look ok? On 11/30/2018 01:14 PM, Figueiro Longo, Maria Gabriela wrote: > > > Hello FreeSurfer Developers, > > I'm attempting to run the longitudinal stream, but in the [LONG] step > of one time-point of on of my subjects, I have the following error: > > MRInormInit(): >

Re: [Freesurfer] mkcontrast-sess and mkcontrast2 matlab errors

what is your $MATLAB variable set to? It should be set to the matlab executable On 11/30/2018 01:30 PM, Emily Levin wrote: > > External Email - Use Caution > > Hi FreeSurfer experts, > > I'm trying to run mkcontrast-sess using the newest development version > of freesufer from Nov 30th,

Re: [Freesurfer] FSGD File

If you want to use the --cache-in option, you need to have run recon-all with the -qcache option. If you take away the -cache-in option, then mris_preproc should run correctly On 11/28/2018 12:45 PM, Larissa Bechtle wrote: > > External Email - Use Caution > > Hi everyone, > thank you

Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

On 11/27/2018 06:46 AM, C.P.E. Rollins wrote: > External Email - Use Caution > Hi Douglas, > > Thanks a lot for your answers. > > 1) For the permutations, would you recommend using this for > controlling for MC in cortical thickness analyses too? Yes > Why is it recommended to use permutation

Re: [Freesurfer] mean LGI per hemisphere

The 2nd row. The value you want is 3.3455 On 11/27/2018 08:19 AM, C.P.E. Rollins wrote: > External Email - Use Caution > > Dear Freesurfer developers, > I have a quick question regarding calculating mean LGI (Marie Schaer's > measure) per hemisphere. > I believe that I can get the mean

Re: [Freesurfer] CerebralWhiteMatterVol {Disarmed}

*From:*freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Greve, > Douglas N.,Ph.D. > *Sent:* Tuesday, November 20, 2018 6:22 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] CerebralWhiteMatterVol > > No, it does no

Re: [Freesurfer] Question regarding mri_label2label and mris_anatomicalstats

Your command looks right. Sometimes there can be some stretching or compression of the labels as it is transformed back to an individual, especially if it is very small. Can you send pics of what you are seeing? On 11/27/2018 05:19 PM, Wang, Xiaoyu wrote: > > External Email - Use

Re: [Freesurfer] Pial sueface error

Is that a subcortical GM structure (eg, amygdala)? The path of the surface in subcort GM structures is unimportant On 11/29/2018 03:17 AM, Miguel Ángel Rivas Fernández wrote: > > External Email - Use Caution > > Hi Freesurfer devs, > > >  I´m doing a visual quality control of my pial and

Re: [Freesurfer] Fw: Surface based paired t test

Right, you can't use --fsgd. The FSGD file is used to get a list of subjects, but you have already specified the list with the --iv options. Does it run properly if you remove --fsgd (but keep --paired-diff)? On 12/06/2018 12:45 PM, john Anderson wrote: > > External Email - Use Caution

Re: [Freesurfer] How to run GLM FIT simulation in parallel?

I don't know what Slurm is, so I guess the answer is no. If you have multiple processors on your machine, you can use the --bg option. In general, I have not seen it take that long to run. How many input subjects do you have? On 12/06/2018 12:55 PM, Sahil Bajaj wrote: > > External

Re: [Freesurfer] Help with Data

On 12/04/2018 02:17 PM, T and LS wrote: > > External Email - Use Caution > > > Dear Help Desk - I have a few basic questions about freesurfer.  I am > retired military bomb technician working on a blast TBI initiative and > not a research so please bear with me.  We are looking at a

Re: [Freesurfer] problem with mri_label2vol

Is this a volume label that is supposed to be on the cortical ribbon? An you wan to do a surface-based dilation? Or do you just want to dilate it in 3D? On 12/04/2018 08:28 PM, Mareike Grotheer wrote: > > External Email - Use Caution > > Hello FreeSurfer Developers, > > I am trying to

Re: [Freesurfer] Fwd: fcseedcor output

Can  you send the full terminal output? On 12/05/2018 01:25 AM, Sara Jafakesh wrote: > > External Email - Use Caution > > > > > > > Dear freesurfer experts, > I want to calculate corrolation between two seeds with > freesurfer-linux-centos6_x86_64_stable_pub-v6

Re: [Freesurfer] Registering Anatomical Parcellation to DWI

Can you be more specific about which files you want to map into your DWI space? Eg, if you want to map wmparc.mgz, then use mri_label2vol. You will need a registration file which you can obtain with bbregister On 12/05/2018 02:34 AM, Maedeh Khalilian wrote: > > External Email - Use

Re: [Freesurfer] hippocampus cortex surface

sorry, we don't have a hippo cortex analysis method On 12/05/2018 10:26 AM, Yixin Ma wrote: > > External Email - Use Caution > > Hi Freesurfer experts, > > After running the segmentation of hippocampus subfields, I'm wondering > if I can get the surface of the gray matter and white

Re: [Freesurfer] fsaverage6 FS6

Try using mris_apply_reg. The command line is simpler (but otherwise gives the same result). On 12/06/2018 11:44 AM, Sanfelici, Rachele wrote: > > External Email - Use Caution > > ​Dear FreeSurfer experts, > > > I am encountering a problem when trying to downsample to fsaverage6 > with

Re: [Freesurfer] Necessity of Matlab for Using FsFast

It is possible to use octave instead with export FS_USE_OCTAVE=1 You must have octave installed of course On 12/05/2018 02:38 AM, Maedeh Khalilian wrote: > > External Email - Use Caution > > Dear experts, > Is it necessary to install Matlab to use FsFast for functional > connectivity? >

Re: [Freesurfer] Surface based paired t test

If you have not sampled the PET data onto the surface, you will need to run mri_coreg to create a registration to the anatomical. Then use can use mris_preproc with the --iv option (listing each subject with a different --iv). Run mris_preproc with --help to get examples On 12/06/2018 12:31

Re: [Freesurfer] fMRI time series extraction

On 12/03/2018 03:14 PM, Zhi Li wrote: > > External Email - Use Caution > > Hello FreeSurfer Experts, > > Now I have a custom annotation file (only the cortical surface). May I > ask how could I use it to extract the mean time series from the > fsfast-preprocessed fMRI data? I have

Re: [Freesurfer] aseg.stats calculations

On 11/20/18 1:37 PM, Song, Da-Yea wrote: External Email - Use Caution Hello, I had a question regarding the aseg.stats and was hoping to get some help. 1. How is the TotalGray calculated? On the wiki page it mentioned that it is the sum of lhCortex + rhCortex + SubCortGray +

Re: [Freesurfer] License issue

did you put it in $FREESURFER_HOME/.license ? Is it world-readable? On 11/20/18 2:38 PM, Sarah Haigh wrote: > External Email - Use Caution > > Hello Freesurfers, > > Can anyone help with a licensing issue I have? I downloaded Freesurfer the > other day with a brand new license and got

Re: [Freesurfer] CerebralWhiteMatterVol

No, it does not. On 11/20/18 3:54 PM, Song, Da-Yea wrote: External Email - Use Caution Hello, Does the CerebralWhiteMatterVol (from the aseg.stats) include the cerebellum? Thank you so much in advance for your help! Best, Da-yea Disclaimer: The

Re: [Freesurfer] Extra-axial CSF and TCV GM

On 11/19/18 7:34 AM, Crocetti, Deana wrote: External Email - Use Caution Hi Folks, 1) Can I derive a measure of extra-axial CSF. I realize this must be generated in order to create the boundary between the skull and dura but not sure if this is saved in as one of the labels. Do you

Re: [Freesurfer] Bonferroni correction of 2spaces or 3spaces

On 11/16/18 7:34 PM, YAN Chao-Gan wrote: External Email - Use Caution Dear freesurfer experts, I have a pretty naive question but would like to confirm. When we use --3spaces option in multiple comparison correction, does that mean we set the Cluster-wise threshold (cwp, not Cluster

Re: [Freesurfer] FDR correction

High p-values (i,e close to 1) mean non-significance. I don't know how to do a power analysis with FDR. On 11/19/18 1:16 PM, Laura Ferrero wrote: > External Email - Use Caution > > Hi, > I performed an statistical analysis comparing autism group with control group > using volume/area

Re: [Freesurfer] Map image in MNI onto fsaverage

You can follow the instructions here for the case where you are not using kinetic modeling. You don't need to do the PVC either https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer This command in particular, you just need to generate the registration and supply you input as the --mov

Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

I can' tell what is going wrong there. Can you run it with --debug as the first option and send the output? BTW, the MC correction for LGI is probably not very accurate. I would recommend using permutation. See here

Re: [Freesurfer] Bonferroni correction of 2spaces or 3spaces

, YAN Chao-Gan wrote: External Email - Use Caution Dear Douglas, When doing --3spaces, is there a default subcortical mask in MNI space provided by freesurfer? Where is it stored? Thanks, Chao-Gan On Tue, Nov 20, 2018 at 10:12 AM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu

Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

can you verify that /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and that you have read permission to it? Eg, can you load it with freeview -f /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white On 11/20/18 8:25 AM, C.P.E. Rollins wrote: External Email - Use Caution

Re: [Freesurfer] Bar/scatter plots for Interaction effects

DEVxSEXxDIA  shows decrease in cortical > thickness at a specific cluster. > Can this be interpreted to be  "the localized  cortical thickness > decrease seen at cluster1 is a result of the interaction of DEVxSEXxDIA" > Thank You > > On Mon, Nov 26, 2018 at 1:51 PM Greve, D

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