[Freesurfer] Subject with extremely large ventricles

External Email - Use Caution Hi Freesurfer Experts, Is there anything that could be done to improve the surface definitions for this particular subject (attached)? The pial and white matter boundaries  in the cortex are generally accurate though. Thank you. Best

[Freesurfer] bbregister on DWI volumes using DOF 12 for epi distortions ?

External Email - Use Caution Hi Freesurfer Experts, I am trying to obtain coregister diffusion data b0 with T1.  One problem is that I do not have any means to correct for EPI distortions. Because of this,  I am experimenting with DOF = 9 and DOF = 12. The mincost for 12 was

[Freesurfer] vol2subfield: which file to use?

External Email - Use Caution Hi Freesurfer Tema, I am trying to use vol2subfield to extract DTI measurements like FA and MD. For this purpose, should I be using the rh.hippoAmygLabels-T1.v21.CA.FSvoxelSpace.mgz or rh.hippoAmygLabels-T1.v21.CA.mgz ? Thank

[Freesurfer] PETSURFER for AV1451

External Email - Use Caution Hi PETSURFERs,  A quick question to the group: Does any one have experience using PETSURFER on dynamic AV1451 scans? How can I know whether the MRTM1 or MRTM2 using midbrains (due to off target AV1451 binding) is suitable for my data?  Thank you!

[Freesurfer] Mri_segstats for PET data: Reviewer question

External Email - Use Caution Hi Freesurfer Team, I have used mri_segstats to get ythe mean PET uptake across all the parcellations in the WMPARC space. These values were calculated in the native PET space (following the DTI tutorial). A reviewer asked what is the grey matter

Re: [Freesurfer] Petsurfer: Motion Correction

External Email - Use Caution Thanks, Doug. I think the command is MCFLIRT. https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MCFLIRT Best Wishes,Shane On Friday, May 3, 2019, 6:18:54 PM GMT+1, Shane Schofield wrote: Hi Freesurfer Team, How may I align 5 volumes of my PET data

[Freesurfer] Petsurfer: Motion Correction

External Email - Use Caution Hi Freesurfer Team, How may I align 5 volumes of my PET data ( 5 min acquisitions each) to a mean image for motion correction across the acquisition? I can use mri_concat to get the the mean image, but I am not sure how to do the realignment after

Re: [Freesurfer] PetSurfer

External Email - Use Caution Hi Doug, thanks for the explanation.  My question is more related to how we might go about knowing what are the high binding regions for any tracer? If I am going to do an FDG-PET study, will the HB region parameters be different from a

[Freesurfer] PetSurfer

External Email - Use Caution Hello PetSurfer Developers On the tutorial page, I do not understand this part: --km-hb 11 12 13 50 51 52 specifies the ROIs to use as the high-binding region if using MRTM2. This creates km.hb.tac.nii.gz with the value for the high-binding region

[Freesurfer] Help with Reviewer Comment

External Email - Use Caution Hi Freesurfer A reviewer asked whether there are concerns about whether Freesurfer may obtain accurate cortical thickness data in people with developmental conditions - the main focus in my study. I did a search and could not find any validation

Re: [Freesurfer] Outlier voxels after partial volume correction using Petsurfer

External Email - Use Caution Hi Doug, it is kinetic modelling, not uptake. Thank you.  On Monday, August 13, 2018, 10:36:13 AM GMT+1, Shane Schofield wrote: Hello Petsurfers! A few of my subjects ended up with vertices that had outlier PET values after I followed

[Freesurfer] Outlier voxels after partial volume correction using Petsurfer

External Email - Use Caution Hello Petsurfers! A few of my subjects ended up with vertices that had outlier PET values after I followed the PetSurfer steps. Most of the binding potentials are in the range of 0 - 3. Looking at the histogram though there are a couple of vertices

[Freesurfer] Longitudinal MRI but different scanner

Hi Freesurfer Team, I try to calculate a within-subject decrease in cortical thickness over 2 years, but the MRI scanner was changed during the project. Is it still possible to do that using the longitudinal stream in Freesurfer?  Thanks. Best

[Freesurfer] Question about mg and mgx

Hi Freesurfer, I have two question about the different partial volume correction options.  Basically how is the --mg method different from the --mgx? I cannot seem to find papers that have compared these methods. Any opinions on this? Does this have any effect on the region of interest GTM

Re: [Freesurfer] Mean diffusivity on cortex?

, 2017, 10:46:09 PM GMT+1, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: SUVR you can. BP is a little trickier because BP estimation is a nonlinear operation that can be biased by noise. Probably it comes out similarly. On 08/16/2017 02:50 PM, Shane Schofield wrote: > Hi

Re: [Freesurfer] Mean diffusivity on cortex?

Hi Dr Greve, On a similar note, can I use the Petsurfer on PET data that have already been averaged into a single frame 3D volume instead of 4D? Example, SUVR and BPND data. Thanks for your help again. On Tuesday, August 15, 2017, 9:09:33 AM GMT+1, Shane Schofield <shane.schofi...@yahoo.

Re: [Freesurfer] Mean diffusivity on cortex?

: You will need to run gtmseg --s subject (takes an hour or so), then add --seg gtmseg.mgz to the cmd line On 08/14/2017 04:12 PM, Shane Schofield wrote: > Hi Dr  Greve, > > Are the settings correct to do partial volume correction of my MD images? > > mri_gtmpvc --i subject/dtr

Re: [Freesurfer] Mean diffusivity on cortex?

out. > > cheers > Bruce > > On Sat, 12 Aug 2017, Shane Schofield wrote: > >> Thank you both. >> >> How can I deal with partial volume in this case? Would it be possible >> to use >> the partial volume tool for PET on my MD volumes? Sorry if it is a silly >

Re: [Freesurfer] Mean diffusivity on cortex?

> maybe Doug's PET stuff. At the very least you should probably regress > thickness out. > > cheers > Bruce > > On Sat, 12 Aug 2017, Shane Schofield wrote: > >> Thank you both. >> >> How can I deal with partial volume in this case? Would it be possible &

Re: [Freesurfer] Mean diffusivity on cortex?

"Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >Hi Shane > >not really - it totally depends on the size of the effect you are looking >for. I would be *very* careful about partial volume effects though > >cheers >Bruce >On Fri, >11 Aug 2017, Shane Sch

Re: [Freesurfer] Mean diffusivity on cortex?

volume. Here you just need the surface-based registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote: > Thanks Dr Yendiki.  > > I am more interested to

Re: [Freesurfer] Mean diffusivity on cortex?

end...@mgh.harvard.edu> wrote: #yiv9314780658 P {margin-top:0;margin-bottom:0;}What effect are you trying to measure with MD on the cortex? From: Shane Schofield [shane.schofi...@yahoo.com] Sent: Friday, August 11, 2017 3:12 AM To: Freesurfer Support List; Yendiki, Anastasia Subject: Re

Re: [Freesurfer] Mean diffusivity on cortex?

on the tutorial. On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield <shane.schofi...@yahoo.com> wrote: Hi DTI Experts, Is it sensible to do comparisons of MD on the cortex surface like a normal cortical thickness comparisons between group? If the answer is yes, are there recom

[Freesurfer] Mean diffusivity on cortex?

Hi DTI Experts, Is it sensible to do comparisons of MD on the cortex surface like a normal cortical thickness comparisons between group? If the answer is yes, are there recommended on smoothing ? DT_RECON has been completed in Freesurfer. Thank you.

[Freesurfer] How to capture missing grey matter after recon-all

Hi Freesurfer Experts, Does anyone know how to deal with situations where the part of the brain is not being captured in aseg.mgz or in the surfaces? I have attached some screenshots. I have tried adding control points but it is not working. Thanks for helping. Best,Shane

Re: [Freesurfer] mri_convert : pix vs no pix ?

, May 9, 2017 5:58 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: When the pixel  data are flipped, you are actually changing the way that the data are stored on disk (while keeping the direction info in the header constant). On 05/09/2017 12:52 PM, Shane Schofield wrote:

[Freesurfer] mri_convert : pix vs no pix ?

Dear Doug,I am trying to flip some PET images so that they are in the same orientation as the T1.I came across this post http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29281.htmlCan you explain what what it means to change the pixel data? Should I use pix or without pix? For

Re: [Freesurfer] How to get SUVR images with cerebellar GM reference?

wrote: add --rescale 7 8 46 47 these are the ids for left and right cblum wm and gm On 04/28/2017 06:13 AM, Shane Schofield wrote: > Hello PetSurfer and Freesurfer Developers, > > I am using PetSurfer to obtain PVC SUVR images . I have already used > mri_concat to derive the mean

[Freesurfer] How to get SUVR images with cerebellar GM reference?

Hello PetSurfer and Freesurfer Developers, I am using PetSurfer to obtain PVC SUVR images . I have already used mri_concat to derive the mean images over three acquisitions (template image). After gtmseg amd mri_coreg, I want to get the SUVR map with whole cerebellum as the reference (instead

Re: [Freesurfer] Filling in missing ventricles in WM

fis...@nmr.mgh.harvard.edu> wrote: yes, that is correct. An alternative would be editing the aseg directly. Editing the wm will help the surfaces but not correct the aseg. But as Antonin suggests, try running with -bigventricles and see if that fixes your problems cheers Bruce On Sun, 23 Apr 2017,

Re: [Freesurfer] bbregister vs spmregister vs mri_coreg

Dear Doug, If I want to create a new volume that is registered to the MNIspace (using mni1525reg), can I mask out other voxels that are not part of the mni template brain? It is a PET volume (already in individual space using bbregister) that has noisy signals in non-brain regions. Thank you.

[Freesurfer] XL defect detected

Hi Freesurfer Team, I am running recon-all on Freesurfer version 6. A few of my subjects have “XL defect detected …” and their recon-all have been running for more than 20 hours. I hope this is not a silly question, but will this XL defect be corrected eventually…?  Another question, what are

Re: [Freesurfer] Mindboggle official software release and publication!

Hello, Thanks. Seems very interesting! Is there any way to run this on Mac? Cheers -- Shane Schofield ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information

[Freesurfer] LGI data for each region?

Hi Freesurfer, How can I get the LGI measurements for each brain region in Desikan atlas? Instead of getting thickness with aparcstats2table, I want the gyrification instead. Thank you. Cheers, Shane --  Shane Schofield___ Freesurfer mailing list

[Freesurfer] mri_glmfit-sim

Hi, I have 3 beginner questions about the use of mri_glmfit-sim 1. Under what type of circumstances should I run mri_glmfit-sim with permutation simulations?  2. The voxel threshold of 0.01 (cache 2) is used a lot. Is this too lenient in cortical thickness comparisons?  3. About the sign of

Re: [Freesurfer] Running recon-all on external hard-disk?

Hi Z K, Thanks. I had thought that the recon-all speed will run much slower on the external HD but 10 hours seems to be the average recon-all time so I am pleasantly surprised. Best Wishes, Shane ___ Freesurfer mailing list

[Freesurfer] Running recon-all on external hard-disk?

Hello, I am new to image analysis and I have a basic question: is it recommended to run recon-all on external hard-disks (USB3.0) to save space on my laptop? Will there be any issues with regards to the performance of recon-all? I have just finished a recon-all on 1 subject and it took me 10