Re: [Freesurfer] Mask custom ROI with automated parcellation (aparc)

works perfectly, thank you! On 28 July 2014 19:27, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Does mri_mask work? On 07/28/2014 12:50 PM, Bastian Cheng wrote: Thank you, Douglas! Is there a way to mask my functional ROI with these binarized aparc ROIs? I guess what I want to do is:

Re: [Freesurfer] LocalGI error {Disarmed}

Hi Doug, I get the following error: Undefined function 'MRIread' for input arguments of type 'char'. Sarina On 29 Jul 2014, at 18:34, Douglas N Greve wrote: a = MRIread('/Volumes/HD-PNTU3/MISSEDDATA/extn003/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz'); Sarina Iwabuchi Division

[Freesurfer] NIH Staff Scientist Position available, Bethesda, MD, USA

Posted on behalf of Dr. Judy Rapoport: Department of Health and Human Services (DHHS) National Institutes of Health (NIH) National Institute of Mental Health (NIMH) Division of Intramural Research Programs (DIRP) Section on Childhood Neuropsychiatric Disorders (SCND) Child Psychiatry Branch (CPB)

Re: [Freesurfer] Freesurfer Start Up

you need a - before each option, so it should be recon-all -help On Wed, 30 Jul 2014, Isaiah C. Smith wrote: The recon-all option is no longer working and neither is the other one. I am getting an error.  Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help ERROR: Flag help unrecognized. help

Re: [Freesurfer] Freesurfer Start Up

Hi Isaiah remove the space. It should be: recon-all cheers Bruce On Wed, 30 Jul 2014, Isaiah C. Smith wrote: The command is not found. Last login: Tue Jul 29 17:42:52 on ttys001 freesurfer-Darwin-lion-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and

Re: [Freesurfer] LocalGI error {Disarmed}

Hi Sarina, you need to have $FREESURFER_HOME/matlab in your matlab path. Try: addpath(sprintf('%s/matlab', getenv('FREESURFER_HOME'))) cheers Bruce On Wed, 30 Jul 2014, Sarina Iwabuchi wrote: Hi Doug, I get the following error: Undefined function 'MRIread' for input arguments of type

Re: [Freesurfer] qdec error

that fixed the problem Thanks Jon From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve gr...@nmr.mgh.harvard.edu Sent: Tuesday, July 29, 2014 4:27 PM To: freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] LocalGI error {Disarmed}

Hi Bruce, It still shows the same error: set: Variable name must begin with a letter. gunzip: Command not found. ERROR: problem reading fname set: Variable name must begin with a letter. rm: Command not found. SWITCH expression must be a scalar or string constant. Error in load_mgh (line 158)

Re: [Freesurfer] LocalGI error {Disarmed}

Is gunzip in your path? When you open a shell and type which gunzip what is printed out? On 07/30/2014 10:45 AM, Sarina Iwabuchi wrote: Hi Bruce, It still shows the same error: set: Variable name must begin with a letter. gunzip: Command not found. ERROR: problem reading fname set:

Re: [Freesurfer] LocalGI error {Disarmed}

And in matlab, what do you get if you type unix('which gunzip') On 07/30/2014 11:08 AM, Sarina Iwabuchi wrote: I get: /usr/bin/gunzip On 30 Jul 2014, at 15:58, Douglas N Greve wrote: Is gunzip in your path? When you open a shell and type which gunzip what is printed out? On

Re: [Freesurfer] LocalGI error {Disarmed}

set: Variable name must begin with a letter. gunzip: Command not found. ans = 1 On 30 Jul 2014, at 16:27, Douglas N Greve wrote: And in matlab, what do you get if you type unix('which gunzip') On 07/30/2014 11:08 AM, Sarina Iwabuchi wrote: I get: /usr/bin/gunzip On

Re: [Freesurfer] LocalGI error {Disarmed}

OK, so there is something going wrong with your unix environment inside of matlab (this is not a freesurfer problem per se). Is there someone around that you can ask about it? Can someone else try this last command to see if it works? There might be something wrong with the resource file of

[Freesurfer] Fwd: mpr2mni305 failed error

I all! I have the same problem in about 15% of MRI scans, all made with the same scanning protocol (T1 MPRAGE in a SIEMENS Avanto 1,5 T) during the recon-all -all process. I can't recognize any difference between those scans which work correctly and those not. I have never found the same error on

Re: [Freesurfer] occipital lobe WM errors

Hey Bruce, I uploaded a subject that you requested a few days ago (problems with segmentation in the occipital lobe). I just wanted to make sure the file transferred successfully, and if you have had a change to analyze. Thanks, Matt On Mon, Jul 28, 2014 at 5:48 PM, Walton, Matt

Re: [Freesurfer] Can't Recognize dicom file

Hi Yi-Yi is this right off the scanner? It looks like it has gone through MIPAV. Can you try one that is right from the scanner? cheers Bruce On Wed, 30 Jul 2014, Yi-Yu Chou wrote: Dear Freesurfer experts: I'm running errors when I try to run the dicom files with recon-all. It shows:

Re: [Freesurfer] Can't Recognize dicom file

Hmm... I got same error message when using the one that is right from the scanner. On Wed, Jul 30, 2014 at 12:17 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Yi-Yi is this right off the scanner? It looks like it has gone through MIPAV. Can you try one that is right from the

[Freesurfer] Voxel Edit Clone Broken in 5.3.0

Hi all, It looks like there’s a bug in Freeview 5.3 Voxel Edit - Clone - although the button is present, the drop down to choose a reference image is unresponsive - you can click it but it doesn’t provide a list of any of the loaded volumes - there’s no way to specify which reference to clone

Re: [Freesurfer] T2-space vs T2-space-FLAIR

Bruce has said the FLAIR might be a little better for FreeSurfer but it¹s worse for myelin maps (has less CNR for the myelin, though you can still see the major areas). Currently, the T2 and FLAIR flags do exactly the same thing, so it doesn¹t even matter what flag you use. I think it depends on

[Freesurfer] mri_binzrize (flag --wm )

Hi, I have a question about the flag -wm in mri_binarize: The following segments IDs 8 2 41 82 251 252 253 254 255 are included in this flag (based on the summary of this command line when I run it). Kindly what is the segment ID (Right-non-WM-hypointensities) means? and why the

Re: [Freesurfer] T2-space vs T2-space-FLAIR

thanks matt, would like to be sure that your comments in relation to the T2-space-flair sequence and not the typical clinical TSE-FLAIR. is that the case? cheers, satra On Wed, Jul 30, 2014 at 2:23 PM, Matt Glasser m...@ma-tea.com wrote: Bruce has said the FLAIR might be a little better for

Re: [Freesurfer] T2-space vs T2-space-FLAIR

Yes we performed both on the same subject in the same session and then compared the myelin map results. Peace, Matt. From: Satrajit Ghosh sa...@mit.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, July 30, 2014 at 1:53 PM To: Freesurfer support list

Re: [Freesurfer] T2-space vs T2-space-FLAIR

thanks matt. cheers, satra On Wed, Jul 30, 2014 at 2:58 PM, Matt Glasser m...@ma-tea.com wrote: Yes we performed both on the same subject in the same session and then compared the myelin map results. Peace, Matt. From: Satrajit Ghosh sa...@mit.edu Reply-To: Freesurfer support list

Re: [Freesurfer] T2-space vs T2-space-FLAIR

Hi Satra I've been working on that this week, and I think the answer is yes, but not a lot. The FLAIR has worked better in our past tests, but I found some problems with the T2 code and it is working much better now, so I think the jury is out. We're happy to give you an alpha version if you

Re: [Freesurfer] mri_binzrize (flag --wm )

Hi Mohamad Right-non-WM-hypointensities are hypointense voxels (in T1 images) in the right hemisphere in regions that are not normally white matter (like the middle of the putamen). I'll leave your other questions for Doug cheers Bruce On Wed, 30 Jul 2014, Alshikho, Mohamad J. wrote:

Re: [Freesurfer] T2-space vs T2-space-FLAIR

please don't count on the T2 and FLAIR options doing the same thing as I suspect that they won't in the near future! Bruce On Wed, 30 Jul 2014, Satrajit Ghosh wrote: thanks matt, would like to be sure that your comments in relation to the T2-space-flair sequence and not the typical clinical

Re: [Freesurfer] T2-space vs T2-space-FLAIR

thanks bruce. we aren't collecting the flair currently but some of our clinical collaborators have asked for it. we are likely to collect both on our next few participants, so happy to test out the alpha version. cheers, satra On Wed, Jul 30, 2014 at 3:08 PM, Bruce Fischl

Re: [Freesurfer] mri_binzrize (flag --wm )

That was an error, 82 should not be in there. doug On 07/30/2014 03:07 PM, Bruce Fischl wrote: Hi Mohamad Right-non-WM-hypointensities are hypointense voxels (in T1 images) in the right hemisphere in regions that are not normally white matter (like the middle of the putamen). I'll leave

Re: [Freesurfer] qdec problem

The DOSS option has been removed (DODS only). Can you give more info about the threshold problem? On 07/30/2014 04:27 AM, Emilia Johansson wrote: Hello, When I use qdec I can´t change the threshold values and I don't have the Design Matrix Type option (DODS, DOSS). I'm using ubuntu

Re: [Freesurfer] qdec _FDR report question (why the result of cluster stats table not match with the statistic map)

what is the contrast stats table and how did you create it? On 07/30/2014 11:35 AM, Wang, Guoying wrote: Dear Freesurfer experts, I am facing the problem to report the significant clusters which was calculated by QDEC. I did the group comparison between healthy and patients in cortical

Re: [Freesurfer] mri_binzrize (flag --wm )

Thank you Doug, Do you mean an error in the script that running this command line ?! kindly what is the number of IDs that I can add after the flag --match ? Mohamad -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On

Re: [Freesurfer] question regarding control point edits

Hi Bruce, Thanks a lot for your help thus far. I've edited, computed, and applied the average bias to the error subjects' orig.mgz files. However, I'm not sure how to re-run all autorecon steps for these cases using the newly created orig.mgz (with bias applied). Thoughts? Thanks, Adam

Re: [Freesurfer] Freesurfer Start Up

Thank you so much, Bruce. I think that I got it. Overall, I am trying to create a source volume conduction model, calculate the lead field matrix, and then create a source model. My instructor said that it might be possible to do this in Freesurfer. Sorry, I am kind of new to using the

Re: [Freesurfer] Freesurfer Start Up

Hi Isaiah you might check out MNE from Matti Hamalainen (ccd). It does all this and more (using FreeSurfer surfaces and segmentations) cheers Bruce On Thu, 31 Jul 2014, Isaiah C. Smith wrote: Thank you so much, Bruce.  I think that I got it. Overall, I am trying to create a source volume

Re: [Freesurfer] yet another newbie question (YANQ)

Hi Donald Yes, you can use mri_convert -rl rawavg.mgz input vol output vol Cheers Bruce On Jul 30, 2014, at 8:12 PM, Krieger, Donald N. krieg...@upmc.edu wrote: Thanks for the helpful responses to the previous questions, Bruce. It’s great to not stay stuck for long. Here’s another.

[Freesurfer] tkmedit error

Dear experts when I use the tkedit, it report the error (in the following). How could I solve it? tkmedit started: Thu Jul 31 10:41:56 2014 /Applications/freesurfer/tktools/tkmedit.bin patient_con_sub126 brainmask.tight.mgz -aux T1.mgz $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $

Re: [Freesurfer] question regarding control point edits

Did it help? Try -make all Cheers Bruce On Jul 30, 2014, at 7:50 PM, Adam Mezher adammez...@gmail.com wrote: Hi Bruce, Thanks a lot for your help thus far. I've edited, computed, and applied the average bias to the error subjects' orig.mgz files. However, I'm not sure how to re-run all

Re: [Freesurfer] Freesurfer Start Up

Thank you, I will go there now. But regarding the output of freesurfer, the format will be .ccd? On Jul 30, 2014, at 7:23 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Isaiah you might check out MNE from Matti Hamalainen (ccd). It does all this and more (using FreeSurfer surfaces