[Freesurfer] How to find the difference between to different fMRI datasets?

Dear FreeSurfer team, Thank you for all your help so far! I would like to visualize the difference between two fMRI data sets. Data set1: Cortical activation during movement of a finger. Data set2: Cortical activation during movement of a finger different from the first finger. How can i

[Freesurfer] Neurohackweek: a summer school for neuroimaging and data science, September 5th-9th 2016

We are happy to announce a call for applications to participate in the first installment of the Neurohackweek summer school for neuroimaging and data science. This 5 day hands-on workshop, held at the University of Washington eScience Institute in Seattle, will focus on technologies used to

Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

Hi Bruce, Thanks for your help. In freeview, the surface outline overlays on the volume correctly, and both the volume and the surface are oriented correctly in terms of R-L, A-P, and S-I axes. In tkmedit, the volume is oriented correctly, but the surface appears to be oriented with some of the

[Freesurfer] mysterious fsgd format error (not the end of line problem)

Hi, I’m having an fsgd error that has totally stumped me. I’m trying to run the following command to compute the second level statistics: mri_glmfit --surf fsaverage lh --y ces.nii.gz --wls cesvar.nii.gz --nii.gz --fsgd RPA-accGT.fsgd --glmdir conVinc_normAcc.wls --C main.mtx --C

Re: [Freesurfer] question about white matter segmentation

nope, you don't have to worry about them if they are not grabbed by the surfaces. cheers Bruce On Mon, 29 Feb 2016, Jasmin Alves wrote: Hello freesurfer support, I have been quality checking after the recon-all command according to the trouble shooting tutorials and have noticed quite a few

[Freesurfer] question about white matter segmentation

Hello freesurfer support, I have been quality checking after the recon-all command according to the trouble shooting tutorials and have noticed quite a few participants that have white matter segmentation occurring on parts of the skull (see screen shot) but these regions are not outlined as

[Freesurfer] AAL atlas question

Hi FS community, I have recon-ed a set of subjects and I was interested in also obtaining structural info (cortical thickness, gray matter volume, surface area etc.) based on a different atlas than the ones FS is using, and in particular the AAL atlas. I was wondering whether my approach would

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi Faezeh, Can you send these in the text of the email. It is very hard to deal with these files? The LUT file shouldn't be an excel file it should be a plain text document (please attach). Thanks, D On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei wrote: > Hi > > Thank you

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi Thank you so much for your response. I attached here three files including the command lines, LUT file , and the list of names I want to get and what the result is actually. I'd appreciate if you look at them and let me know what is wrong with that. Regards, Faezeh Vedaei On Mon, Feb 29,

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi Faezeh, Please provide more details (those i described in the earlier email). Thanks d On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei wrote: > Hi, > > I checked again to arrange the labels in the order of LUT file, but the > result has not changed. Can you help me more

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi, I checked again to arrange the labels in the order of LUT file, but the result has not changed. Can you help me more how I can fix this problem? Thank you so much for your time and help. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei wrote: >

Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

Hi John when you say that they are oriented correctly in freeview, does that mean that they just overlay properly on the volume? Or that e.g. what freeview thinks is anterior is actually anterior, etc...? cheers Bruce On Mon, 29 Feb 2016, John Plass wrote: Hello Freesurfer Experts, I

[Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

Hello Freesurfer Experts, I wrote in recently about my parcellation troubles with an ex-vivo scan ( link ). Digging further, I've found that the surfaces I've produced following the Ex-Vivo recon instructions

Re: [Freesurfer] Using N3 MNI and N3 FS corrections

Hi Adam I don't think we know. It's probably ok, but you'll just have to try it out Bruce On Mon, 29 Feb 2016, Adam Martersteck wrote: Hi Freesurfer users, I have a question about using the N3 algorithm twice for processing ADNI data: Is it okay for data to have undergone the ADNI N3

[Freesurfer] Using N3 MNI and N3 FS corrections

Hi Freesurfer users, I have a question about using the N3 algorithm twice for processing ADNI data: Is it okay for data to have undergone the ADNI N3 correction (Boyes et al. 2008 http://www.ncbi.nlm.nih.gov/pubmed/18063391) AND then pushed through the Freesurfer pipeline and undergo FS N3

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi Faeze, It is difficult to help without more details, but in my experience, (exact command, the color lut file in text in the email and what the error in the naming was, which label went to which entry in the color lut.) You need to put the labels in the order of your custom color lut file.

Re: [Freesurfer] Patch for ribbon.mgz failure

try copying this to $FREESURFER_HOME/bin ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats On 02/24/2016 01:21 PM, Philip Deming wrote: > > Hi Freesurfer team, > > > I'm having an issue running -autorecon2. The program exits with errors > because it is unable to create

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi, Thank you for your response. Yes, you are right. The names come from the color LUT file. But, the issue is that I chose the label files from that LUT file too. It meas the source that I chose the label files from and the source of the region's names in tksurfer are the same. The problem is

Re: [Freesurfer] Corrupted head surface with mkheadsurf?

try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize On 02/23/2016 10:17 AM, Maheen Siddiqui wrote: > I changed the directory and it ran, but with errors. I had to change > the last part --surf lh.seghead --surf-smooth 10 because it does not > recognise

[Freesurfer] Doubts with Longitudinal Analysis Repeated Measures ANOVA

Dear FS Experts, I'm interested in performing Repeated Measures ANOVA 2x2. I have 2 groups and two times (pre and post treatment). I have checked the tutorial for repeated measures anova and previous emails: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg45703.HTML

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi Faeze, I believe the name comes from the Color LUT file. Try changing the name in there. hth d On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei wrote: > Hi Freesurfer experts, > > I have created an annotation file by several label files using > mris_label2annot command

[Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi Freesurfer experts, I have created an annotation file by several label files using mris_label2annot command in Freesurfer. The problem is that when I open this annot file in tksurfer and click on colored regions which corresponded to specific labels I had chosen them, I do not have their name

[Freesurfer] Patch for ribbon.mgz failure

Freesurfer community, I'd like to repost a question I asked last week, regarding a failure to create the ribbon.mgz file in -autorecon2. The release notes for 5.3 indicate a patch should fix this: Creation of the aseg.stats table fails when only running -autorecon1 or -autorecon2 because

Re: [Freesurfer] number of vertices

Thanks! That number helps. Just want to get an approx. number in general. Best, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu On 2/29/16, 11:52 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl"

Re: [Freesurfer] number of vertices

it's usually a bit less than that - aroudn 140K or so Bruce On Mon, 29 Feb 2016, Yang, Daniel wrote: > Hi Bruce, > > Is it okay to say that it is approximately 160,000 vertices per > hemisphere? I found the answer from a paper >

[Freesurfer] number of vertices

Dear FreeSurfer experts, Can you please indicate the number of vertices FreeSurfer use in each hemisphere to reconstruct the brain (e.g., cortical thickness)? Is there a fixed number or an approx. number? Many thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail:

Re: [Freesurfer] number of vertices

Hi Bruce, Is it okay to say that it is approximately 160,000 vertices per hemisphere? I found the answer from a paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3824100/pdf/fnhum-07-00722.pdf ). Best, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu

Re: [Freesurfer] number of vertices

Hi Daniel the number of vertices will vary depending on the surface area and geometry of the white matter for each hemisphere. cheers Bruce On Mon, 29 Feb 2016, Yang, Daniel wrote: Dear FreeSurfer experts, Can you please indicate the number of vertices FreeSurfer use in each hemisphere

Re: [Freesurfer] How to invoke skullstrip adjustments and wm control points

Hi Ed just run them once - it will detect the manual interventions and preserve them. cheers Bruce On Mon, 29 Feb 2016, Ed Gronenschild wrote: Hi Bruce, I'm confused about this. The manual-intervention workflow directives listed in recon-all (6 beta) tell that the series of commands should

Re: [Freesurfer] How to invoke skullstrip adjustments and wm control points

Hi Bruce, I'm confused about this. The manual-intervention workflow directives listed in recon-all (6 beta) tell that the series of commands should be: -autorecon2 -autorecon2-cp -autorecon3 -autorecon2 processes stages 6-23 and -autorecon2-cp process stages 12-23 So it seems to be a waste of