Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)

Dear Doug, Unfortunately, it doesn't make a difference if I'm using a dot or comma or simply type in 2 or 3 as a threshold. The terminal output always shows me the converted version with a comma 2.3 --> 2,3 or 2 --> 2,0 which is not recognized by the command. Maybe I have to change the defaul

Re: [Freesurfer] subcortical segmentation only

Dear Bruce! Thanks a lot for the response. I try to get an idea about the minimal time needed to get the subcortical volumes. Best wishes, Luke > Re: [Freesurfer] subcortical segmentation only > Bruce Fischl Wed, 10 Dec 2014 05:22:18 -0800 > > Hi Luke > > you can run -autorecon1 and -autoreco

Re: [Freesurfer] use of high res T1 for subcortical segmentation

Dear Remi! Would you mind to send me the new mri_tessellate? Best wishes, Luke > Re: [Freesurfer] use of high res T1 for subcortical segmentation > Remi Gau Wed, 10 Dec 2014 06:29:04 -0800 > > Hey, > > Someone corrects me if I am wrong, but it seems that the number of > vertices currently all

[Freesurfer] Qdec coordinates

Dear experts, I had a question regarding the output of my Qdec analyses. When I run a Monte Carlo Z simulation on my results, I get the following output: # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZCWP CWPLowCWPHi NVtxs Annot 12.930 94685921.76-48.9

Re: [Freesurfer] retinotopy analysis viewing problem in Freesurfer 5

Thank you very much! The map opened by rtview seems correct. As a new learner of retinotopic analysis, I have one more basic quesion: What do the three files (imag.nii.gz, real.nii.gz and fsig.nii.gz) represent? Hope some experienced one can reply me! Mingxia On Thu, Dec 11, 2014 at 12:14 AM, Do

[Freesurfer] QDEC, Correction for multiple comparisons

Hello,everyone Your reply said I can't use alphasim with qdec.By the way ,Could I use alphasim in other ways in FreeSurfer,for example command line ? Best regards. Xin-Fa Shi. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.

Re: [Freesurfer] Getting voxel values from aseg.mgz

mri_extract_label Usage: mri_extract_label [options]... Options: -s apply a Gaussian smoothing kernel -t apply the transform in to extracted volume -exit_none_foundexit 1 if label(s) not found -dilate dilate output volume times

Re: [Freesurfer] use of high res T1 for subcortical segmentation

if you tell us what hardware/software platform you want it for we can post the current version, which I think has a limit of 10,000,000 vertices and twice that many faces. Presumably that is enough? cheers Bruce On Thu, 11 Dec 2014, lukas.sch...@ukb.uni-bonn.de wrote: Dear Remi! Would y

Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

Hello, Has anyone had a chance to look at this? I still haven't been able to solve the problem. Thanks! Lindsay On Mon, Dec 1, 2014 at 2:41 PM, lindsay hanford wrote: > Hello Freesurfer Experts! > > I am encountering the dreaded mri_glmfit error: matrix is ill-conditioned > or badly scaled, c

Re: [Freesurfer] use of high res T1 for subcortical segmentation

Hi Bruce! I am working on a Mac, OS 10.10.1, FS version: freesurfer-Darwin-lion-stable-pub-v5.3.0 All the best, Luke > Re: [Freesurfer] use of high res T1 for subcortical segmentation > Bruce Fischl Thu, 11 Dec 2014 05:36:52 -0800 > > if you tell us what hardware/software platform you want it

Re: [Freesurfer] Problem with mris_register: face not in vertex face list

Hi Bruce, Thank you very much for this information. Deleting the rh.sphere file and re-running -make all did fix this issue and the brain now looks great. I wanted to confirm this so that if anyone else has the same issue they will know what might work to fix it. I had a question about the pot

Re: [Freesurfer] Problem with mris_register: face not in vertex face list

Hi Ezra I have no idea why this would have happened. That's plenty of disk space and RAM. sorry Bruce On Thu, 11 Dec 2014, Wegbreit, Ezra wrote: Hi Bruce, Thank you very much for this information.  Deleting the rh.sphere file and re-running -make all did fix this issue and the brain now lo

Re: [Freesurfer] Problem with mris_register: face not in vertex face list

No worries. Just checking to make sure there wasn't something I missed. I appreciate your help, as I now have a workaround in case this issue recurs. Best wishes, Ezra *___* *Ezra Wegbreit, PhD* NIMH T32 Post-doctoral Research Fellow in Ch

Re: [Freesurfer] retinotopy analysis viewing problem in Freesurfer 5

imag is the imaginary (sine) part of the signal real is the real part (cosine) fsig is the significance (-log10(p)) where p is computed from an F test of the real and imag components On 12/11/2014 05:09 AM, zhang mingxia wrote: > Thank you very much! > > The map opened by rtview seems correct.

Re: [Freesurfer] Tracula_critical issue

Hi Mohamad - What you did with your binarization was that you lowered the threshold all the way to zero, i.e., included all the voxels that had any probability > 0 to be in the tract. This means that you included more voxels than the default, which is to threshold at 20% of the max probability.

Re: [Freesurfer] TRACULA- DKI?

Hi Cat - Currently the only stats that are produced automatically are FA/MD/RD/AD. But if you have volumes of other parameters, you could always use the tracts from trac-all and extract mean values of those parameters within each tract with something like mri_segstats, fslastats, etc. Best, a.

Re: [Freesurfer] TRACULA mask error

Hi Amanda - The final masks used by tracula are derived from the structural and not the diffusion data, i.e., they are the whole-brain FreeSurfer segmentations (from mri/aparc+aseg.mgz) mapped onto diffusion space and dilated slightly. It may be that there was something wrong with the FreeSurf

Re: [Freesurfer] TRACULA with Philips par-rec format

Hi - Any format that can be handled by mri_convert (run "mri_convert --help" to see the list) can be run through freesurfer and tracula. If mri_convert doesn't work on your format, you'll have to find a converter that can convert it into one of the formats on that list (like nifti). Hope thi

Re: [Freesurfer] Command '-qa' in TRACULA

Hi Anri - This is not a command itself, it's an option of the trac-all command. So you need to run: trac-all -qa -c the_name_of_your_configuration_file Or, if you just run the entire preprocessing: trac-all -prep -c the_name_of_your_configuration_file then the motion QA measure

Re: [Freesurfer] TRACULA fmajor recon failure: needing help

Hi Emad - Those missing voxels in the mask in the middle of the corpus callosum could very well be what's not allowing that tract to be preconstructed. The file used to create the brain mask from the freesurfer recon is not mri/brainmask.mgz, but mri/aparc+aseg.mgz, which is mapped to diffus

Re: [Freesurfer] trac-all -path error "Segmentation Fault (Core Dumped)"

Hi Thomas - No bother at all! If you search for the word "error" in your trac-all.log, you'll see that it couldn't find the MNI template, which means that some of the pre-processing steps did not complete. You can either remove the "mnitemp" line from your configuration file (so that it uses t

Re: [Freesurfer] Question re. Tracula motion measures

Hi - The fact that the first 2 parameters are all zero (translation and rotation) means that it didn't find the file that it expects to derive those parameters from. Currently, this is the eddy_correct log file that contains the affine registration matrices from each DWI volume to the first vo

Re: [Freesurfer] From bedpostX and recon-all to tracula

Hi Kate - The screenshot looks more like a low-b image from a diffusion scan than a field map. In case this helps, the phase map data will have either 2 volumes (2 phase maps acquired at different echo times) or 1 volume (the difference of 2 such phase maps). Best, a.y On Thu, 11 Dec 2014,

Re: [Freesurfer] From bedpostX and recon-all to tracula

I am sorry, I am a bit confused. What am I supposed to be specifying under the b0mlist and b0plist? I thought that it was the B0 low-b image from diffusion. Thank you! On Thu, Dec 11, 2014 at 2:25 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Kate - The screenshot looks mo

Re: [Freesurfer] From bedpostX and recon-all to tracula

No, those are field maps used to correct for inhomogeneities in the main magnetic field (which in MRI lingo is referred to as the B0 field, not to be confused with the b=0 images). You can skip that correction (you have to skip it if you don't have field maps). On Thu, 11 Dec 2014, Katherine

Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

Your FSGD file appears to have been made under windows or using an editor that is not simple text. The contrast matrix looks ok. doug On 12/01/2014 02:41 PM, lindsay hanford wrote: > Hello Freesurfer Experts! > > I am encountering the dreaded mri_glmfit error: matrix is > ill-conditioned or b

Re: [Freesurfer] QDEC, Correction for multiple comparisons

No On 12/11/2014 06:48 AM, Xinfa Shi wrote: > Hello,everyone > > Your reply said I can't use alphasim with qdec.By the way ,Could I use > alphasim in other ways in FreeSurfer,for example command line ? > > Best regards. > > Xin-Fa Shi. > > > ___ > Frees

Re: [Freesurfer] QDEC cluster stats

You should run mri_glmfit-sim from the command line passing it the QDEC glmdir as output and the same thresholds you used in QDEC. This will create several output files one of which will include the means inside each cluster. Run it with --help to get more info. doug On 12/10/2014 12:16 PM, W

Re: [Freesurfer] Can one adjust CWP Threshold in Qdec?

Once you have the CWP image loaded, the Threshold value sets the CWP. doug On 12/03/2014 10:12 AM, Claire Morley wrote: > Hi Freesurfer Experts, > I was wondering if there is a way for me to adjust the default CWP of > p <.01 to p <.05 on Qdec? I saw that it is possible using cwpvalthresh > .05

[Freesurfer] obtaining the level of smoothness in the data

Hi all, I'd like to know whether there is a command line that I could use to extract the level of smoothness in my data, the same way qdec does it automatically, i.e. writing the fwhm.dat that is then used to define which precomputed CSD file should be used in the Monte Carlo Simulation. Is th

Re: [Freesurfer] obtaining the level of smoothness in the data

Hi Marie, you can use mris_fwhm, something like mris_fwhm --i y.mgh --subject fsaverage --hemi lh --cortex --dat fwhm.dat doug On 12/11/14 8:40 PM, Marie Schaer wrote: > Hi all, > > I'd like to know whether there is a command line that I could use to extract > the level of smoothness in my dat

Re: [Freesurfer] Command '-qa' in TRACULA

Thanks, Anastasia. I'm worried about that a quality assessment step is not run because there are no presentation about "-qa" when I type "trac-all" in terminal (other steps are presented.) Do you mean QA step will be run even if no mention about it? Thanks in advance, Anri

Re: [Freesurfer] obtaining the level of smoothness in the data

Awesome Doug, that's exactly what I wanted, thanks a lot for the prompt answer! Have a nice evening, Marie On Dec 11, 2014, at 6:38 PM, Douglas Greve wrote: > > Hi Marie, you can use mris_fwhm, something like > > mris_fwhm --i y.mgh --subject fsaverage --hemi lh --cortex --dat fwhm.dat >

Re: [Freesurfer] Command '-qa' in TRACULA

I tried to run trac-all -qa -c the_name_of_my_configuration_file after trac-all -corr -c the_name_of_my_configuration_file, but it failed. I pasted the log below and do you have any advices? Thank you, Anri [watanabeanris-Mac-Pro:~] watanabeanri% trac-all -corr -c $TUTORIAL_DATA/diffusion_tutori