Re: [Freesurfer] recon-all

On 11/5/15 8:37 AM, John Anderson wrote: Thanks a lot Doug! Kindly ... 1. What do you mean by intensity normalized? Removing non-biological intensity fluctuations such as darkening/brightening from multiple head coils 2. What is the purpose of conforming the inputs to 256^3 1mm3 This is

Re: [Freesurfer] MatrixReadTxT: could not scan value [1][1], ERROR: loading C AAA.mtx

can you send the matrix? On 11/5/15 5:29 AM, Erik Lindberg wrote: Dear Freesufer experts, I have trouble loading a contrast matrix - however I am not sure if something is going wrong earlier ... and this is causing this problem. Below is the error messages that I get plus the contrast

[Freesurfer] MatrixReadTxT: could not scan value [1][1], ERROR: loading C AAA.mtx

Dear Freesufer experts, I have trouble loading a contrast matrix - however I am not sure if something is going wrong earlier ... and this is causing this problem. Below is the error messages that I get plus the contrast matrix and the .fsgd file I am trying to run. I checked this previous

Re: [Freesurfer] hello freesurfer developer~

are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm images from *different* series or from the *same* series? If they are in the same series than that explains what is happening. You should only give recon-all a single file

Re: [Freesurfer] mri_convert and large values

Hi Stephanie, can you send me one of your dicoms? doug On 11/5/15 11:27 AM, McMains, Stephanie wrote: We are finding a conversion problem with our latest multiband/SMS data (Using a sequence from Minnesota). The values can be very large, greater than 53,000. These large voxels get turned

Re: [Freesurfer] segmentation question

There is no separate label for Wernike's (it is a functional, not anatomical, definition). Heschl's gyrus is separate from STG. Perhaps Christophe can weigh in on his labels. On 11/5/15 11:42 AM, Ahtam, Banu wrote: Dear All, I am new to freesurfer and would appreciate your help with the

[Freesurfer] Recon-all with lower resolution T2 / Proton Density reconstructions and higher res T1

Hello Freesurfer experts, I am working with a database of pre-collected scans. Although the T1 images are collected at 1x1x1 mm^3 resolution, the T2 and proton density scans are .938x.938x3 mm^3. 1) I wanted to see if you think that using the T2 scans for recon-all would hurt or help the

[Freesurfer] segmentation question

Dear All, I am new to freesurfer and would appreciate your help with the following questions. I tried to look through the previous posts but couldn’t find the answers to all my questions. Thank you in advance. Best, Banu My question: I wanted to look at certain language related regions

Re: [Freesurfer] Recon-all with lower resolution T2 / Proton Density reconstructions and higher res T1

1. We don't have much experience with this. 3mm is pretty thick so it may not work, but the only way to find out is to try 2. I'll leave this for Eugenio. 3. Yes, I think it could help, although note that part of the point of using T1/T2 is that the bias field cancels cheers Bruce On Thu,

[Freesurfer] Trackvis/ DTK Tracula question

Hi Anastasia: I processed 42 brains on Tracula and it ran without problems. I am now trying to run them individually on DTK to test another hypothesis. [I am using the DTK for the first time]. I loaded the diffusion weighted image, filled the parameters in the GUI and ran one single brain.

[Freesurfer] Fwd: REMINDER: OHBM 2016 Call For Council Nominations Deadline Nov. 9

Forwarded Message Subject:REMINDER: OHBM 2016 Call For Council Nominations Deadline Nov. 9 Date: Thu, 05 Nov 2015 11:36:37 -0600 From: i...@humanbrainmapping.org Reply-To: i...@humanbrainmapping.org To: gr...@nmr.mgh.harvard.edu Dear OHBM Member: Your

Re: [Freesurfer] the matrix

The contents of the AAA.mtx matrix are {1 1 1 1 -1 -1 -1 -1}/4 0 It has to be a simple matrix with simple numbers, no characters, no math symbols. It will not do the math for you. On 11/05/2015 05:12 PM, Erik Lindberg wrote: > Dear Doug, > attached is the folder I tried to run with the

Re: [Freesurfer] aparcstats2table

white On 11/05/2015 04:18 PM, Yang, Daniel wrote: > Dear FreeSurfer Experts, > > When I perform aparcstats2table —meas area, does it get it pial.area > or white area? > > I believe it is the pial.area, but this is not documented. If yes, > what can I obtain white area via aparcstats2table? > >

Re: [Freesurfer] R: Re: R: Re: error MRS voxel as seed in FS-FAST

How many non-zero voxels are in MRS_MASK.mgz? Is MRS_MASK.mgz 256^3, 1mm3 ? On 11/05/2015 04:47 PM, std...@virgilio.it wrote: > Please see the file attached. > Thanks > > Stefanofile > > Messaggio originale > Da: gr...@nmr.mgh.harvard.edu > Data: 5-nov-2015 15.43 > A:

Re: [Freesurfer] the matrix

make sure there are no blank lines On 11/5/15 6:29 PM, Erik Lindberg wrote: OK, however I tried several options. With the matrix 1 1 1 1 -1 -1 -1 -1 0(using the doss option for age) I basically get the same results Reshaping mriglm->mask... search space = 74612.446501 MatrixReadTxT:

Re: [Freesurfer] interaction in glm

On 11/04/2015 05:10 AM, Erik Lindberg wrote: > > Dear Freesurfer experts, > > I know this has been an ongoing topic in the mailing list – however I > would like to raise the issue one more time. In the choice between > doss and dods – I usually check if there is a significant interaction >

[Freesurfer] aparcstats2table

Dear FreeSurfer Experts, When I perform aparcstats2table —meas area, does it get it pial.area or white area? I believe it is the pial.area, but this is not documented. If yes, what can I obtain white area via aparcstats2table? Thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center

[Freesurfer] R: Re: R: Re: error MRS voxel as seed in FS-FAST

Please see the file attached.Thanks Stefanofile Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 5-nov-2015 15.43 A: Ogg: Re: [Freesurfer] R: Re: error MRS voxel as seed in FS-FAST sorry, should have been fcseed-sess -debug -s

[Freesurfer] extract pial surface

Dear experts, how can I extract pial surface (in mm2) of all our participants? Performing aparcstats2table -meas area extracts white area. Thanks, Sandy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] extract pial surface

The area.pial file. Best, Feng 发件人：Sandy Schramm 发送时间：2015-11-06 15:24 主题：[Freesurfer] extract pial surface 收件人："freesurfer" 抄送： Dear experts, how can I extract pial surface (in mm2) of all our participants? Performing

Re: [Freesurfer] R: Re: error MRS voxel as seed in FS-FAST

sorry, should have been fcseed-sess -debug -s Control22_FS -cfg MRS_MASK.config |& tee doug.log On 11/4/15 6:05 PM, std...@virgilio.it wrote: Hi Dough, in summary: I have the MRS_MASK.mgz within $SUBJECTS_DIR/Control22/mri thus, I have copy this file in fMRI directory (fMRI/Control22_FS) the

[Freesurfer] Job: OHSU Fair Neuroimaging Lab Research Associate

Damien Fair's Neuroimaging Lab is looking for a candidate with expertise in neuroimaging, particularly in the field of MRI. While the main focus of this position is in neuroimaging, candidates with experience in bioinformatics and software development are highly encouraged to apply. The

Re: [Freesurfer] recon-all

Thanks a lot Doug! Kindly  ... 1. What do you mean by intensity normalized? 2. What is the purpose of conforming the inputs to 256^3 1mm3 3. In order to move mask to diffusion space (FA map) or PET space I do the following:            3.1 I register FA map to T1 ( after converting the DICOMs