Re: [Freesurfer] Multiple comparison question

Hi VM, They can stay all in the same .csv file. The "fwep" files will have p-values corrected across all columns of this input. All the best, Anderson On 2 February 2017 at 12:09, neuroimage analyst < neuroimage.anal...@gmail.com> wrote: > Thanks, Anderson. If there are several other

Re: [Freesurfer] Error: if: Expression Syntax.

Why are you passing a dicom file as the registration file? The reg file is a FS-specific text file used to store the registration matrix. On 2/2/17 6:35 PM, Anderson Napolitano wrote: Hello Experts! I am having trouble running the following command: tkregisterfv --mov

Re: [Freesurfer] CUDA in FS6?

I have tested a recon-all -all CPU and GPU with and without the -hires option and everything seems to run fine. So at the moment they seem to be compatible or at least the GPU version doesn't crash. So that is ok. Thanks for your time. Dr Chris Adamson Research Officer, Developmental Imaging,

Re: [Freesurfer] CUDA in FS6?

On 1 February 2017 at 22:07, Chris Adamson wrote: > I understand they are not a priority. But are they compatible with the CPU > versions? Should we be using the CUDA versions if they aren't guaranteed to > be up-to-date? I haven't run any comparisons against the

Re: [Freesurfer] license file not working

Strange, that fixed things right up for me. You might make sure you know where you are calling FreeSurfer from and that there are no old license files lying around. Peace, Matt. From: on behalf of Anthony Dick Reply-To: Freesurfer

Re: [Freesurfer] license file not working

Thanks Matt. I already tried it with a new registration, but it doesn't hurt to try it again. That may be where the issue is. I'll post if that turns out to be the problem. Thanks! Anthony On 2/2/17 6:28 PM, Matt Glasser wrote: Like I said, they changed the format at some point and stopped

[Freesurfer] Error: if: Expression Syntax.

Hello Experts! I am having trouble running the following command: tkregisterfv --mov /Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016002B/IM-0001-0001.dcm --reg

Re: [Freesurfer] license file not working

Like I said, they changed the format at some point and stopped accepting the old format with FS 6.0. I have used FreeSurfer for a long time too and found that I had to get a new license file with this version. Peace, Matt. From: on behalf of Anthony

Re: [Freesurfer] license file not working

Hello, I have used my old file, registered under two different emails (and received the code and made new files each time, named both .license and license.txt). Restarted the computer etc. I am wondering if it is a permissions issue. It seems to be finding the file where I put it. Have never

Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6)

Hi Joe there are slight differences, and for sure we reserve the right to use the knowledge that it is a FLAIR scan in the algorithms, so you should probably rerun cheers Bruce On Thu, 2 Feb 2017, Joe Necus (PGR) wrote: > > Hello, > > > I am running recon-all on the latest version of

Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6)

It will behave differently as some of the parameters change depending upon whether it is a T2 or FLAIR. This will only affect the surface creation On 02/02/2017 05:19 PM, Joe Necus (PGR) wrote: > > Hello, > > > I am running recon-all on the latest version of freesurfer (Version 6) > and would

[Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6)

Hello, I am running recon-all on the latest version of freesurfer (Version 6) and would like to know whether there is any difference between using the -T2 -T2Pial and -Flair flags. I am currently running recon-all with a T1 and FLAIR image, but have used the -T2 -T2pial flags and would like

Re: [Freesurfer] design specification with 3 categorical predictors

The second design is fine if there is no significant interaction between 1 or 2 and 3. You'll have to create the design matrix yourself or you can create an fsgd file with 7 classes On 02/02/2017 11:38 AM, Tim Reess wrote: > > Dear Freesurfer experts, > > I would like to set up a design matrix

Re: [Freesurfer] LGI issue/Error

So ismac.m is not defined in your matlab implementation? What version of matlab are you using? What kind of computer are you running on? On 02/02/2017 01:48 PM, aral ahmadi wrote: > > Dear experts > > I have a question regarding Freesurfer- LGI error I got during running > LGI after all recon

Re: [Freesurfer] Group connectivity maps with crazy sig values

I don't think there is anything really wrong. There are computation limits on the maximum significance. When the given voxel goes beyond that, I set it to this ridiculously high level. This high level just means that it is really significant. On 02/02/2017 12:18 PM, Rodriguez-Thompson, Anais

Re: [Freesurfer] possible atlas error to report

Sorry, which labels are consistent and which are inconsistent? On 02/02/2017 02:52 PM, Levman, Jacob wrote: > > Hi there, > > > I've been conducting an asymmetry analysis based on FreeSurfer > measurements. There are regions of the brain with known left-right > asymmetry such as BA44 which

Re: [Freesurfer] license file not working

The .license that it comes with is not the same as the license.txt that you have to acquire. I was able to use an old license.txt from my Freesurfer 5.3 for 6.0. Best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Thu, Feb 2, 2017 at 3:21 PM, X

Re: [Freesurfer] How to check recon-all finished without any error

Try checking your recon all.log in your scripts folder of the subject. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Thu, Feb 2, 2017 at 1:52 PM, shi yao wang wrote: > Dear FS experts: > How to check recon-all

Re: [Freesurfer] ROIs in midline for cortical thickness

Thanks Dr. Fischl. I will surely give a try to this. On Wed, Feb 1, 2017 at 3:17 PM, Bruce Fischl wrote: > I see. Have you run recon-all on each hemi? If so, use bbregister to > register the surfaces to the fmri data, then use mri_vol2surf to map the > activations on

Re: [Freesurfer] Analysis of rates or percent changes

Hi Martin, I dropped --generic-time flag as you suggested in the previous e-mail and run the long_stats_slopes command again like this: long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats aseg.stats --meas volume --sd $SUBJECTS_DIR --do-rate --do-pc1fit --do-pc1

Re: [Freesurfer] CUDA in FS6?

Richard, I understand they are not a priority. But are they compatible with the CPU versions? Should we be using the CUDA versions if they aren't guaranteed to be up-to-date? Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens

[Freesurfer] Multiple comparison question

Hi, We extracted volume measures from 7 ROIs in 2 groups and compared a) Mean of each ROI volume between group, and compared independently such as i) whether mean of ROI 1 in group 1 is equal to mean of ROI1 in group 2 ii)whether mean of ROI 2 in group 1 is equal to mean of ROI2 in group 2 and

[Freesurfer] Neighborhood thickness in a 10mm radius

Hi Freesurfers, Thank you for the help you provide through this list. Is there a way to get, for each vertex, the identify (or thickness values) of the surrounding vertices in a 10mm radius? The command mris_convert has the '-v' option, but that produces only 5-6 vertices and there is no option

Re: [Freesurfer] license file not working

They updated the format so you have to get another. Peace, Matt. On 2/2/17, 2:13 PM, "Anthony Dick" wrote: >Hello, > >I have been using Freesurfer for a number of years, and just installed >v6.0. I run into this problem: >

Re: [Freesurfer] license file not working

try to rename the file to license.txt? On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick wrote: > Hello, > > I have been using Freesurfer for a number of years, and just installed > v6.0. I run into this problem: > >

[Freesurfer] license file not working

Hello, I have been using Freesurfer for a number of years, and just installed v6.0. I run into this problem: -- ERROR: Invalid FreeSurfer license key found in license file /Applications/freesurfer/.license If you are

[Freesurfer] possible atlas error to report

Hi there, I've been conducting an asymmetry analysis based on FreeSurfer measurements. There are regions of the brain with known left-right asymmetry such as BA44 which exhibits strong leftward asymmetry (the left side is bigger than the right). This is accurately reflected when you compare

[Freesurfer] Cannot find CTF archive

Dear FS experts: when I running hippocampus subfield, I got error messages:" Cannot find CTF archive". I copied command and screen to you. Thank you very much! [silun.wang@node5 N01]$ *recon-all -s N01 -hippocampal-subfields-T1* Subject Stamp:

[Freesurfer] How to check recon-all finished without any error

Dear FS experts: How to check recon-all finished without any error? Sometime, there are showing no error message, however, when I running hippocampus subfield, it does not run. thanks Lawrence Emory ___ Freesurfer mailing list

[Freesurfer] LGI issue/Error

Dear experts I have a question regarding Freesurfer- LGI error I got during running LGI after all recon steps been ran with no problem. you could see the error below. *reading filled volume...* *??? undefined function or variable 'ismac'.* *error in -->load_mgh at 68*

[Freesurfer] Freesurfer- LGI error

Dear experts, I have a question regarding Freesurfer- LGI error I got during running LGI after all recon steps been ran with no problem. Attached you could see the error. The error is ...Undefined function or variable 'ismac' - matlab is expecting that variable to be defined (it's trying to

[Freesurfer] design specification with 3 categorical predictors

Dear Freesurfer experts, I would like to set up a design matrix for a design that is not QDEC-able. I have three categorical factors: 1.disease status: 2 levels 2.gender: 2 levels 3.scan site: 4 levels The first design I set up was the following (the rows are just for illustration and

Re: [Freesurfer] Multiple comparison question

Thanks, Anderson. If there are several other measures such as volume, thickness, FA, can I then put them in a single csv file and run the command or I have to create 3 csv files, one each for volume, thickness,and FA and also invoke -corrmod? Thanks Regards VM On Feb 2, 2017 1:01 AM, "Anderson

Re: [Freesurfer] Multiple comparison question

Hi VM, Please see below: On 1 February 2017 at 02:38, neuroimage analyst < neuroimage.anal...@gmail.com> wrote: > Hi, > > We extracted volume measures from 7 ROIs in 2 groups and compared > a) Mean of each ROI volume between group, and compared independently such > as > i) whether mean of ROI

Re: [Freesurfer] longitudinal tracula error

Thanks again — it was a huge help! On 31 Jan 2017, at 18:25, Yendiki, Anastasia > wrote: Hi Barbara – Thank you for your kind words. As you’ve read, if the output files are generated, then you’re good to go. Bedpost does not