Re: [Freesurfer] surface based analysis (projfrac)

Yes On 01/13/2017 03:28 PM, John Anderson wrote: > Thank you Doug for the advice , > I will follow your pipeline, I see that the command "gtmseg " is part > of Freesurfer 6. Can I apply it on recons generated by Freesurfer 5.3 ? > Best, > John > *Sent:* Friday, January 13, 2017 at 3:16 PM >

Re: [Freesurfer] surface based analysis (projfrac)

Thank you Doug for the advice , I will follow your pipeline, I see that the command  "gtmseg " is part of Freesurfer 6. Can I apply it on recons generated by Freesurfer 5.3 ?   Best, John Sent: Friday, January 13, 2017 at 3:16 PM From: "Douglas N Greve" To: 

Re: [Freesurfer] surface based analysis (projfrac)

I am working on surface-based analysis to study the differnce in PET signal in the cortex between two groups. When I used "projfrac=0.5 " there was no differnce between the groups at "cwp 0.05", and when I changed the "projfrac to 0" I got significant differnce between the groups in specific

Re: [Freesurfer] surface based analysis (projfrac)

These differences are hard to track down because they are so subtle. You may want to use our PET module, which includes PVC http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer On 01/13/2017 03:10 PM, John Anderson wrote: > I am working on surface-based analysis to study the differnce in PET >

Re: [Freesurfer] surface based analysis (projfrac)

What is the modality you are looking at? On 01/13/2017 02:08 PM, John Anderson wrote: > Thank you very much Doug, > Kindly, do you suggest me any steps to avoid patial volume effects in > surface based analyses ? > Best, > John > *Sent:* Friday, January 13, 2017 at 12:21 PM > *From:* "Douglas N

[Freesurfer] aparc stats file output

Dear Freesurfer users, I have a question on the 'aparc.stats' file output: Which of your label corresponds to: Ventro and Dorso Lateral Prefrontal Cortex? Supplementary motor areas? Putamen? Angular Gyrus? Thank you for your help Sincerely, Marianna

Re: [Freesurfer] QDEC table import issue

It was the spaces! Thanks for the help On Jan 13, 2017, at 11:40 AM, Douglas N Greve > wrote: I'm not sure that QDEC can read in a CSV file. Can you remove the commas and try again? You'll also have to remove the spaces between column

Re: [Freesurfer] surface based analysis (projfrac)

Thank you very much Doug, Kindly, do you suggest me any steps to avoid patial volume effects in surface based analyses ?   Best, John    Sent: Friday, January 13, 2017 at 12:21 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer]

Re: [Freesurfer] QDEC table import issue

I'm not sure that QDEC can read in a CSV file. Can you remove the commas and try again? You'll also have to remove the spaces between column headings On 01/13/2017 10:55 AM, Paul Rowley wrote: > Good morning, > I’m experiencing issues importing data into QDEC. When I upload the table, > this

Re: [Freesurfer] surface based analysis (projfrac)

On 01/12/2017 05:20 PM, John Anderson wrote: > Thank you very much Doug and thank you for briniging the issue of > "partial volume effect " to my attention. Kindly, I have one last > question. > I found in wiki that the default values for projfrc value are between > 0 and 1. Are there

Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream

Hi Martin, Thank you for the clarification. I assume this participant should be removed? As a rule of thumb, should I exclude participants who have a total of 3% scaling? Is there a way to check potential scaling problems (e.g. looking into the recon-all.log to see scaling or checking alignment

Re: [Freesurfer] Reviewer questions...

Dear FreeSurfer experts, Thankyou so much for your prompt and comprehensive responses! They are excellent and will definitely guide me in how to respond to the Reviewers of my manuscript. Kind regards, Jerome On 14 January 2017 at 01:03, Iglesias Gonzalez, Eugenio < e.igles...@ucl.ac.uk>

Re: [Freesurfer] Reviewer questions...

Thanks for your good points, Antonin. More on the matter: When segmenting standard resolution (~ 1mm) T1 scans, the position of the internal boundaries between the hippocampal substructures largely relies on prior knowledge acquired from our ex vivo training data and summarized in our

Re: [Freesurfer] -cw256 and -hires

Hi Chris are you talking about recon-all -hires ...? That has worked for me without cropping to 256. cheers Bruce On Fri, 13 Jan 2017, Chris Adamson wrote: In the git version I’m trying to use the -hires option on an image. It initially says that I need the cw256 option to restrict the

[Freesurfer] Covariates / rmANOVA

Hello, we are trying to use covariates while calculating a rmANOVA as described in https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova. Is this technically possible with freesurfer? Thank you, best regards, René ___ Freesurfer mailing

Re: [Freesurfer] TRACULA in FreeSurfer 6.0 trac-paths error

Hi Derek - Thanks for testing the 6.0 release candidate. Does it keep running after this message? Since this is a warning and not an error, it may not be critical. If you run mri_info on your dwi.nii.gz, does the TE show up as zero? Best, a.y From:

[Freesurfer] QDEC table import issue

Good morning, I’m experiencing issues importing data into QDEC. When I upload the table, this is the error I receive: Loading data table /Applications/freesurfer/subjects/qdec/qdec.table.dat... Number of columns: 10 fsid column:1 Number of factors: 9 Number of subjects: 19 ERROR: