[Freesurfer] Problems with the .Qdecrc file

Hi, i am trying to add new measures (pial_lgi) to qdec. I created the .Qdecrc file in my SUBJECTS_DIR/qdec, with the described text (MEASURE1 = pial_lgi), but it does not work, i cannot select in the qdec menu pial_lgi as a dependent variable. A qdec.fsgd file is also in the same place.

[Freesurfer] Atlas coordinates provided by QDEC

Hi FreeSurfer experts, I have a doubt regarding the atlas coordinates that uses QDEC. In the power point titulated fscoordinates found in the FreeSurferWiki seems that the coordinates used are aligned with Talairach Atlas, but when you enter de coordinates provided by QDEC in a particular area

Re: [Freesurfer] Mri_concat: initial frame ok but noisy in output image

Hi, Thank you for your help! I think there might be something wrong just with the display, as in fact more brains looked strange. I have re-run the concatenation with the same commands after killing many processes on my computer and now all brains look correct and in the expected order. Cheers,

Re: [Freesurfer] longitudinal version

Hi Natalia, the images in 5.0 are not in the same voxel space across time. Probably that is what's causing your problems. In 5.1 they are all resampled and processed in the subjects' template space. So you cannot simply open stuff on top of each other with 5.0 data. However, surfaces are in

[Freesurfer] Problems with segmentation

Hi freesurfers After checking recon-all -autorecon-all processing, I realized that a part of the duramadre has been not fully removed (please see attached file). Can anyone help me how to solve this please. Best regards. -- Leo Kay. attachment:

Re: [Freesurfer] long_mris_slopes error

Hi Derin, there is a know and fixed bug in mris_calc in the 5.1 release. It has difficulties with very long file names and returns a non zero exit code, which stops my script in some situations. I'll ask Nick if he can put up a fixed version of mris_calc for download. Best, Martin On Thu,

Re: [Freesurfer] Error in qdec longitudinal 5.1

Hi Natalia, check your qdec/.QDECRC file, it needs to contain: MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc probably you put a .spc instead of -spc Best, Martin On Fri, 2011-07-22 at 18:51 +0200, Natalia h wrote:

Re: [Freesurfer] Problems with segmentation

Hi Leo if the pial surface is in the right place in those regions you don't have to worry about it. cheers Bruce On Mon, 25 Jul 2011, leonardo kay wrote: Hi freesurfers After checking recon-all -autorecon-all processing, I realized that a part of the duramadre has been not fully removed

[Freesurfer] Qdec does not change the color bar though the color scare is reversed on the brain.

Hi I have a problem when using qdec. When I check the option reverse values there color on the brain switch color, but the color bar stays the same. Is there anything that might be wrongs in my files? Is there anything that I might edit in Qdec configuration file? I do not know what kind of log

Re: [Freesurfer] Pial Edits on Base Template

Hi, yes, rerunning with force in this case is correct. If you made edits to cross and want to rerun base, I would recommend to delete the base first and recreate it from scratch. Any edits in the base will not be meaningful anyway as the images (and maybe even the space) will change underneath.

[Freesurfer] QC Montages error

Hello, I have tried troubleshooting this problem in various ways, but I am still not able to figure out the problem. I probably gave more output than necessary. Does anyone have any idea? Thank you! I am getting an error when using a script that combines these 3 actions: preproc.sh

Re: [Freesurfer] QC Montages error

Hi Chindhuri, I don't know anything about those scripts (I don't think that they are distributed with FS). Why are you using version 4? doug Chindhuri Selvadurai wrote: Hello, I have tried troubleshooting this problem in various ways, but I am still not able to figure out the problem. I

Re: [Freesurfer] QC Montages error

Hi Chindhuri, I don't think we have access to that path where the scripts are. Double-check the path names in your script, it looks like some of the path names are relative. Also, make sure you are running the script from the right directory to begin with. -Louis On Mon, 25 Jul 2011,

Re: [Freesurfer] Converting from volume label RAS to Talairach

That almost works; tkmedit is giving talairach coordinates of, for a few examples: 14.7 23.9 -22.3 24.8 21.9 -18.8 35.6 20.8 -20.9 54.2 14.1 -17.1 61.1 10.9 -9.6 62.3 6.0 -1.8 Running mri_label2label with fsaverage as the target subject yields a label in which those same points have the

[Freesurfer] ROI analysis with label in both hemispheres -still looking for an answer

I'm still looking for an answer on this. If the answer is you can't do it, I'm ok with that, I just would like to know! Thanks! Hi all, I was wondering if anyone had any idea if it was possible to combine together ROIs from the separate hemispheres into one ROI (for example LH V1 and RH V1)

Re: [Freesurfer] ROI analysis with label in both hemispheres -still looking for an answer

Hi Katie, you could do it in the volume, but I doubt there's any way to do it on the surface. cheers Bruce On Mon, 25 Jul 2011, Katie Bettencourt wrote: I'm still looking for an answer on this.  If the answer is you can't do it, I'm ok with that, I just would like to know!  Thanks!

[Freesurfer] Dimension error - mri_segstats

Hi freesurfers, I performed ROI cortical thickness measurements earlier on an older version of FS as described on http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness and I was able to get the required values. Now I have the latest version of FS. I draw an ROI mask using FSL

Re: [Freesurfer] Qdec does not change the color bar though the color scare is reversed on the brain.

HI I have reproduce the error by using the group data from buckner_tutorials. The files may be download from this link with the error http://vedlegg.uib.no/?id=0c18c8445e29c173fcf02a208ca1c255 and with none reversal of values http://vedlegg.uib.no/?id=20e06d09dcc450ff4abcd85e1e5ab1c5. Is there a

Re: [Freesurfer] ROI analysis with label in both hemispheres -still looking for an answer

Are there instructions for how to do volume functional analysis and how to do it that way? I've only ever done surface based analysis. Katie On Mon, Jul 25, 2011 at 3:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Katie, you could do it in the volume, but I doubt there's any way to

Re: [Freesurfer] Dimension error - mri_segstats

appreciated. Is there any other workflow to define a volume ROI and then get the cortical thickness in the area. Thanks! Jaichander -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110725/b2ca0802

[Freesurfer] lesion question

Hello everyone, I have several patients with large cortical lesions (haemorrhage). I want to have subcortical structure volumes reflect the lesion, i.e. show up as hypointensities in aseg.mgz (which they're not right now). However I also want to calculate cortical thickness, and the WM GM

[Freesurfer] WM and ASEG edition... recon-all continue command...

Hi I editted the wm.mgz and aseg.mgz files... Which recon-all command must I use to continue the processing ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] WM and ASEG edition... recon-all continue command...

-make all should work. cheers Bruce On Mon, 25 Jul 2011, Gonzalo Rojas Costa wrote: Hi I editted the wm.mgz and aseg.mgz files... Which recon-all command must I use to continue the processing ?... Sincerely, Gonzalo Rojas Costa ___

[Freesurfer] mri_surfcluster coordinates

Dear Freesurfers, I know that Qdec outputs coordinates in a Freesurfer specific space, rather than in Talairach space, per this old thread https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-November/008878.html However, I found that mri_surfcluster (Freesurfer v5.0) in its summary

Re: [Freesurfer] WM and ASEG edition... recon-all continue command...

Hi Bruce: Maybe I didn't explain clearly my question... I did a complete processing of a patient, then I must edit wm.mgz and aseg.mgz because I found some segmentation errors... Which recon-all command must I run to reprocess the study to use the edited files (wm.mgz and aseg.mgz) ?...

Re: [Freesurfer] Qdec does not change the color bar though the color scare is reversed on the brain.

I sent a wrong link. The correct link is here. I have gone through the tutorials using qdec and when I reverse the values the color bar is not reversed. With reversed color values age verse thickens http://tjinfo.uib.no/Vedlegg?id=9720b934c5a5a437924453ddb23497b2 Without reversed color