Re: [Freesurfer] trac-all error

2019-10-21 Thread Yendiki, Anastasia
The error message in your log file ("dyld: Symbol not found...") has been addressed here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61247.html From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of nayan wadhwani Sent: Tuesday, October 2

Re: [Freesurfer] trac-all error

2019-10-21 Thread Yendiki, Anastasia
Please attach your log file from scripts/trac-all.log. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of nayan wadhwani Sent: Tuesday, October 22, 2019 1:13 AM To: Freesurfer support list Subject: Re: [Freesurfer] trac-all error External Email

Re: [Freesurfer] trac-all error

2019-10-21 Thread nayan wadhwani
External Email - Use Caution Hello Freesurfer, I did changes asked by you but still error persists. While i am using dicom images why it is asking for NIFTI format. I checked the lib folder also and checked and all the files mention above are there in the folder. Do i need to che

[Freesurfer] how to get the full name of cortical segmentation structures?

2019-10-21 Thread chen
External Email - Use Caution Dear freesurfer experts, I want to know the full name of the cortical segmentation structures. The look up table cannot solve my question. For example, the full name of the rh_bankssts_volume or rh_parsopercularis_volume. Cheers, Chen_

Re: [Freesurfer] tracula FA question - 2 cohorts/2 scanners

2019-10-21 Thread Krieger, Donald N.
External Email - Use Caution Thanks for getting back on this. Best - Don From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Yendiki, Anastasia Sent: Monday, October 21, 2019 10:25 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] tracula FA question - 2

Re: [Freesurfer] trac-all error

2019-10-21 Thread Yendiki, Anastasia
Hi Nayan - Try using /Applications instead of $Applications everywhere. Also, the config file seems to be in rich text format - not sure how that'll work. Try converting it to plain text (if you use mac, from the Format menu of the text editor). Best, Anastasia.

Re: [Freesurfer] tracula FA question - 2 cohorts/2 scanners

2019-10-21 Thread Yendiki, Anastasia
Hi Don - Diffusivity and FA depend on the b-value. Even if you just scan a subject with multiple b-values on a single scanner, and you compute FA etc from each shell, you'll get different values in the same voxel. So this is unrelated to what tractography method you use, tracula or other. There

[Freesurfer] Converting ROIs from MNI152 space to MNI305

2019-10-21 Thread Barbour, Tracy,M.D.
Hello experts, I am trying to convert insula ROIs that are in MNI 152 2 mm space to MNI305 space. I will eventually this ROI for connectivity analysis. I ran mri_vol2vol: mri_vol2vol --mov $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --targ /autofs/cluster/neuromod/Insula_ROIs/left/k10/cl

Re: [Freesurfer] [EXTERNAL] Freesurfer Digest, Vol 188, Issue 32

2019-10-21 Thread Xie, Hong
External Email - Use Caution Thank you -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of freesurfer-requ...@nmr.mgh.harvard.edu Sent: Monday, October 21, 2019 10:33 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Freesurfer Digest, V

[Freesurfer] subcortical volume-based pet analysis

2019-10-21 Thread miracle ozzoude
External Email - Use Caution Hello Experts, I do have couple questions about using mri_glmfit and mri_glmfit-sim for this analysis based on the tutorial page. https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer 1) Do i have to add any other flags when using mri_glmfit for this an

[Freesurfer] Incorrect/Negative Hippocampal subfields volumes

2019-10-21 Thread Jayachandra Raghava
External Email - Use Caution Hello Freesurfer experts & Eugenio, I have been trying to extract the volumes of hippocampal subfields using the longitudinal pipeline ( https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields) on macOS Mojave using freesurfer-Darwin

[Freesurfer] tracula FA question - 2 cohorts/2 scanners

2019-10-21 Thread Krieger, Donald N.
External Email - Use Caution I have tracula runs on two cohorts whose imaging was obtained on different scanners with slightly different beta's and other parameters. Would the differences in the scanners and scanning parameters be expected to produce large cohort-wide differences

Re: [Freesurfer] FreeSurfer transforms

2019-10-21 Thread Vinny K
External Email - Use Caution Ok thanks for the suggestions. On Sun, Oct 20, 2019 at 3:11 PM Bruce Fischl wrote: > I see. Yes, a bunch of those are on our to-do list for segmentation but > we don't have anything distributable at the moment. You are probably > better off running s

Re: [Freesurfer] FSGD file formatting for Xhemi

2019-10-21 Thread Jose Graterol
External Email - Use Caution Thanks for your answer. I want to correlate TMS values in 17 stroke patients. Following the instructions provided to Anders in this link https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+flipping+s

Re: [Freesurfer] aseg.stats format FreeSurfer 5 versus 6

2019-10-21 Thread Tim Schäfer
External Email - Use Caution Hi Doug, thanks for the confirmation! All the best, Tim > On October 18, 2019 at 4:01 PM "Greve, Douglas N.,Ph.D." > wrote: > > > They are just different names > > On 10/17/19 11:52 AM, Tim Schäfer wrote: > > External Email - Use Cauti