Re: [Freesurfer] colour scale

how else would you suggest I generate a colour bar? tksurfer doesn't appear to be working for me either. Best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Mon, Sep 12, 2016 at 7:53 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill.ca>

Re: [Freesurfer] colour scale

thanks! -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Mon, Sep 12, 2016 at 7:24 PM, Ruopeng Wang wrote: > It appears you are running version 5.3. The upcoming 6.0 should fix it. > > On Sep 12, 2016, at 5:34 PM, Trisanna Sprung-Much < > trisanna.sprung-m.

Re: [Freesurfer] colour scale

It appears you are running version 5.3. The upcoming 6.0 should fix it. > On Sep 12, 2016, at 5:34 PM, Trisanna Sprung-Much > wrote: > > Hi there > > yup, so I had seen that. The issue is it looks like this and doesn't seem to > change no matter what changes I make in the GUI (heat vs colour

[Freesurfer] Pial surface vs. aparc+aseg

Hi, I'm very new to Freesurfer, and I am trying to get subject-specific masks from the output of recon all that I can use on my functional data. I was going to isolate regions from the aparc+aseg files to create the ROIs. In my visual checks, I noticed that the pial surface often leaves off par

[Freesurfer] Job posting

DEPARTMENT OF VETERANS AFFAIRS Palo Alto WRIISC Special Postdoctoral Fellowship Program in Advanced Neuroimaging The Office of Academic Affiliations, Department of Veterans Affairs (VA), is now accepting applications for a two-year Postdoctoral Fellowship Training Program in advanced neuroimaging

Re: [Freesurfer] colour scale

There is a color bar button on the toolbar, or you can go to menu View->Show Color Scale. Ruopeng On 09/12/2016 03:50 PM, Trisanna Sprung-Much wrote: Hi there is there a way to view a colour scale bar in Freeview rather than Tksurfer, for instance, for a probability map? I can alter the Min

[Freesurfer] Postdoc and Research Assistant openings in cognitive neuroscience at UCSF/Stanford

Please respond to i...@brainlens.org *Research Assistant Position at UCSF in California, USA on Multilingualism* The Hoeft Lab (http://brainLENS.org PI: Fumiko Hoeft MD PhD) is looking for an exceptional research assistant interested in the developmental cognitive neurosci

Re: [Freesurfer] Analysis of rates or percent changes

Hi Martin, Thanks a lot. Best, Katarina Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia From: freesurfer-boun...@nmr.mgh.harvard.edu o

[Freesurfer] colour scale

Hi there is there a way to view a colour scale bar in Freeview rather than Tksurfer, for instance, for a probability map? I can alter the Min and Max by "Configure Overlay" but cannot seem to display the bar next to my surface. Many thanks Trisanna -- Ph.D. Candidate McGill University Integrat

Re: [Freesurfer] Fwd: Tkregister2 error, moveable not present just white screen

I think the problem is the initialization. I noticed you used --init-header. This should only be used if the two volumes were acquired during the same session and the direction cosines (ie, geometry) info is accurate for both. Is this the case? I noticed that the input has "preproc" in the name

[Freesurfer] convert FSFAST files to gifti format

Hi all, Is there a way to convert FSFAST files (fmcpr.odd.sm5.fsaverage.?h.nii.gz) files to convert into gifti format? I've tried mris_convert but it does not work. Thanks for help. Cheers, Sabin Khadka ___ Freesurfer mailing list Freesurfer@nmr.mgh.ha

Re: [Freesurfer] mris_anatomical_stats

Hi Bruce, Thank you so much for this suggestion. In case anyone searches for this thread in the future, I am writing back to report that it worked and thickness indices remain the same (although other indices, which are of no interest to me for this analysis, did change). Best, Arkadiy _

Re: [Freesurfer] Qdec Error: Couldn't open qcache file

I have already solved the problem. Thank you for your support. Best regards Jana Dinges -- Diese Nachricht wurde von meinem Android Mobiltelefon mit GMX Mail gesendet.Am 07.09.16, 23:57, Douglas N Greve schrieb: *Can you send the terminal output for recon-all -s subjid -qcache*

Re: [Freesurfer] ERROR again

normalization means to subtract the mean and divide by the stddev On 09/12/2016 02:04 PM, Seung Gul Kang wrote: > Dear Douglas Greve and FS team, > > I send this e-mail again since I was afraid that you would not receive > my previous e-mail. > I am sorry if you got the previous e-mail and are

Re: [Freesurfer] Analysis of rates or percent changes

Hi Katarina, different time spacing is OK (not optimal, but OK). This 2-stage procedure first fits a line in each subject, independent on how many time points the subject has. Of course a linear fit from 4 time points will be more reliable than one from just 2 time points. This is not taken

[Freesurfer] ERROR again

Dear Douglas Greve and FS team, I send this e-mail again since I was afraid that you would not receive my previous e-mail. I am sorry if you got the previous e-mail and are figuring this problem out. I am looking forward to receive your reply regarding to the solution. Thank you. Best, Seung-G

Re: [Freesurfer] Getting Waveform from Label - dim mismatch

you need to transfer the label into the space of subject 401 using mri_label2label. Currently, the label is in fsaverage space which is why you get the mismatch On 09/12/2016 12:53 PM, ERIK JAHNER wrote: > (sorry if you got this multiple times this morning I had some server > issues) > > I had

Re: [Freesurfer] Tracula movement

You're right that this looks fine. Can you upload the entire DWI series for me here? Nifti is fine. Thanks! https://gate.nmr.mgh.harvard.edu/filedrop2/ On Mon, 12 Sep 2016, Lars M. Rimol wrote: Re: [Freesurfer] Tracula movement Anastasia Yendiki Mon, 12 Sep 2016 04:24

[Freesurfer] Fwd: Tkregister2 error, moveable not present just white screen

Hi Doug I can't see any errors in the log file, and with other datasets I did not have this issue. My register.dat is: 50664 3.00 4.50 0.15 9.996076822280884e-01 -2.117119915783405e-02 -1.833262108266354e-02 3.139470825195312e+02 1.872027479112148e-02 1.825972087681293e-02 9.996579289

[Freesurfer] Getting Waveform from Label - dim mismatch

(sorry if you got this multiple times this morning I had some server issues) I had not seen a post based on this email, so I am resending it. It is my understanding that I can use freesurfer and FSfast to get activation levels after data has been smoothed across the surface instead of 3D volume.

[Freesurfer] Analysis of rates or percent changes

Hi, I have a question about the analysis of rates or percent changes. I use data with available scans at baseline (TP1) and the 6-month (TP2), 12-month (TP3) and 24-month (TP4) follow-ups from ADNI dataset. An example of some of the data in the appropriate qdec table is given below: fsid fs

Re: [Freesurfer] [martinos-tech] Trobles witg GLM Surface-based Cluster Summary Table

you can find it here fsaverage/surf/?h.white.avg.area.mgh On 09/12/2016 11:26 AM, Claudia Dacquino claudia.dacqu...@gmail.com [martinos-tech] wrote: > Thanks Doug! > Yes, I realized I was wrong and I wrote to the freesurfer list too. > Just another question,as you were so prompt in replying...

[Freesurfer] visualize corrected results

Dear FS, I have a question on visualizing results from GLM analysis... How can I visualize corrected results in Freeview after having applied bonferroni/FDR correction (somewhere else)? I saw it is not possible (error: masking file missing) -and was told it is not necessary- to apply monte carl

Re: [Freesurfer] [martinos-tech] Trobles witg GLM Surface-based Cluster Summary Table

Hi Claudia, it is better to post these things to the freesurfer list as martinos-tech is no longer active. The total cortical surface area (65416.6mm2) is incorrect. The total should be 82219.960938. The reported value is the actual surface area of the fsaverage white surface. However, the aver

Re: [Freesurfer] mris_anatomical_stats

I think that would be ok, but an easy way to test it is to try it on another subject first with their actual wm.mgz, then with the one from fsaverage to check that the thickness is the same. cheers Bruce On Sun, 11 Sep 2016, Arkadiy Maksimovskiy wrote: > Dear Freesurfer Experts, > > I am tryi

Re: [Freesurfer] Coordinates of particular volumes

Hi Aziz, make sure $FREESURFER_HOME/matlab is in your matlab path. cheers Bruce On Mon, 12 Sep 2016, Aziz Nanthaamornphong wrote: Which the version of Matlab has a 'MRIread' function? I got this error message from my installed Matlab (v. 8.4.0).  "Undefined function 'MRIread' for input argu

[Freesurfer] Troubles witg GLM Surface-based Cluster Summary Table

Hi all, I've run GLM surface analysis and I've got a summary table like this: # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # CreationTime 2016/09/12-08:47:18-GMT #

Re: [Freesurfer] Tracula movement

Hi Lars - This sounds like the subject was trying to climb out of the scanner: 3cm average translational motion and 24% of the slices in the series have drop-out. How do the images look? a.y On Mon, 12 Sep 2016, Lars M. Rimol wrote: HI, Is there a rule-of-thumb upper level of acceptable he

[Freesurfer] Tracula movement

HI, Is there a rule-of-thumb upper level of acceptable head motion? The tutorial gives these values as examples: AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore 0.489419 0.00398925 0 1 I have a subject with AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore *30.018* 0.209

Re: [Freesurfer] Parcelation a2009 as mask for SPM analysis

Hi Doug, Yes I did and the registration looks good to me (no axial shift in the images) - but I am little confused. In the command for check the registration: /tkregister2 --mov $SUBJECTS_DIR/568/mri/mni152.orig.mgz \ --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_

Re: [Freesurfer] Coordinates of particular volumes

Which the version of Matlab has a 'MRIread' function? I got this error message from my installed Matlab (v. 8.4.0). "Undefined function 'MRIread' for input arguments of type 'char'." Best Regards, Aziz. On Mon, Sep 5, 2016 at 6:46 AM, Bruce Fischl wrote: > yup, or mri_Info called form the comm