[Freesurfer] Hippocampus Segmentation Troubleshoot - Matlab crash

External Email - Use Caution Hi there, I am a Master's student who is looking to segment the hippocampus and analyze diffusion data of the segments. I am trying to utilize the segmentation function with this command: segmentHA_T1.sh subj01 But I am met with this error saying that

Re: [Freesurfer] Freesurfer crash when loading "volume" surf

this? Thank you, M On Fri, Oct 27, 2023 at 7:44 AM Wang, Ruopeng wrote: > Can you load a MRI volume? From the crash report, it seems to be a system > related issue that triggered the crash. > > Ruopeng > > On Oct 26, 2023, at 8:42 PM, Mirsol Choi wrote: > > Exte

[Freesurfer] dt_recon question

External Email - Use Caution Hi there, I am currently going through the dt_recon tutorial on your website and I just have a quick question regarding the recon-all and dt_recon commands on freesurfer. For me to process dt_recon, my understanding is that I must process recon-all fi

[Freesurfer] Finding Intracranial volume

External Email - Use Caution Hi fellow freesurfers! I am a Masters student currently working with diffusion images. I would like to ask you experts how I can obtain ICV from my T1/T2 or diffusion images. Is there a certain output from recon-all that produces intracranial volume?

Re: [Freesurfer] Finding Intracranial volume

__ > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Mirsol Choi < > mir...@ualberta.ca> > Sent: Wednesday, November 1, 2023 5:23 PM > To: Freesurfer support list > Subject: [Freesurfer] Finding In

[Freesurfer] Mapping input volume (fa.nii) to hippocampus segmentation volume

External Email - Use Caution Hello Freesurfers, I am trying to segment the hippocampus into its subfields and take the FA values from each subfield area. I am able to segment the hippocampus using the command (segmentHA_T1.sh) and I was also able to perform the dt-recon function

[Freesurfer] vol2subfield troubleshoot

External Email - Use Caution Hello Freesurfers, My name is Mirsol and I am currently trying to obtain FA values from particular hippocampus subfields by registering our fractional anisotropy map (FA.nii.gz) from dt_recon command and our hippocampus segmentations from the command s

[Freesurfer] Cannot locate reg.lta

External Email - Use Caution Hi there, I am currently trying to run vol2subfield command that allows us to get a registration between an input volume (ie. FA map) to a subfield volume (hippocampus segmentation). Upon tying vol2subfield --help, this was the message provided: "vol

Re: [Freesurfer] Cannot locate reg.lta

External Email - Use Caution Thank you for your prompt response! On Tue, Nov 28, 2023 at 5:07 PM Douglas N. Greve wrote: > You have to create your own registration. Eg, try bbregister > > On 11/28/2023 6:42 PM, Mirsol Choi wrote: > > External Email - Use

[Freesurfer] Converting register.dat file to reg.lta

External Email - Use Caution Hello there, I am wondering if there is a way to convert register.dat file produced from dt_recon to reg.lta. I need a reg.lta file that contains registration between the DTI data and processed (recon-all) T1 data. I have tried to perform bbregister,

Re: [Freesurfer] Converting register.dat file to reg.lta

rom:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Mirsol Choi > *Sent:* Wednesday, November 29, 2023 5:19 PM > *To:* Freesurfer support list > *Subject:* [Freesurfer] Converting register.dat file to reg.lta > > > >

Re: [Freesurfer] Converting register.dat file to reg.lta

gt; > specify trg image geometry > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Mirsol Choi > *Sent:* Wednesday, November 29, 2023 5:32 PM > *To:* Freesurfer support lis

[Freesurfer] Sample registration question

External Email - Use Caution Hi there Freesurfer, I am currently using freesurfer to take DTI metrics (FA, MD) from hippocampal subfields. At this point of my exploration with freesurfer, I am able to correctly register the hippocampal subfields and diffusion data, and obtain my F

Re: [Freesurfer] Sample registration question

re > you saying you want to do a voxel-based analysis (without reference to > ROIs)? > > On 1/9/2024 12:05 PM, Mirsol Choi wrote: > > External Email - Use Caution > > Hi there Freesurfer, > > I am currently using freesurfer to take DTI metrics (FA, MD) from > hip

Re: [Freesurfer] Sample registration question

z > --sum fa-in-subfields.dat > > > > On 1/12/2024 4:53 PM, Mirsol Choi wrote: > > External Email - Use Caution > Hi there, > > Is there a way to successfully obtain FA/MD values from the hippocampus > subfields? > > Thank you, > M > > > On Fri, J

Re: [Freesurfer] Sample registration question

Douglas N. Greve wrote: > oh, I thought you wanted to do an ROI analysis. You mean for a voxelwise > analysis? > > On 1/12/2024 5:46 PM, Mirsol Choi wrote: > > External Email - Use Caution > Hi there, > > > Following the first registration step, should I a

Re: [Freesurfer] Sample registration question

an you want to do > a voxelwise analysis but only inside, eg, whole hippocampus? > > On 1/12/2024 6:07 PM, Mirsol Choi wrote: > > External Email - Use Caution > Hello, > > Sorry I should have clarified. Yes, I would like to perform voxelwise > analysis of FA and

Re: [Freesurfer] Sample registration question

External Email - Use Caution Thank you for taking the time to respond on a weekend. On Sat, Jan 13, 2024 at 11:00 AM Mirsol Choi wrote: > Hello, > > My goal is to compare the FA and MD values of hippocampal subfields (only > inside the hippocampus) between cognit