Re: [Freesurfer] question about recon-all

you can put it on our ftp site: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange but at that point you might as well tar and gzip the entire subject dir and upload it On Wed, 31 May 2017, Jasmin Alves wrote: Hi Bruce, Thanks for the reply, below is a couple of sentences from the re

Re: [Freesurfer] label file from freesurfer 5.3

Thank you so much for your help! -- Y.J. Daniel Yang, Ph.D. Assistant Research Professor Autism and Neurodevelopmental Disorders Institute The George Washington University and Children’s National Health System E-mail: daniely...@gwu.edu > On May 31, 2017, at 3:24 PM, B

Re: [Freesurfer] question about recon-all

Hi Jasmin typically that means there is a big topological defect, which definitely can be caused by motion. What is the last couple of lines of the recon-all.log file of one of the subjects? Can you upload an image we can look at? cheers Bruce On Wed, 31 May 2017, Jasmin Alves wrote: H

Re: [Freesurfer] label file from freesurfer 5.3

sure. Easy enough to do in matlab. On Wed, 31 May 2017, Daniel Yang wrote: Thanks, Bruce! It works now. Is it possible I can convert all the negative values in the label to something like 1? Best, Daniel --  Y.J. Daniel Yang, Ph.D. Assistant Research Professor Autism and Neurodevelopmental Diso

Re: [Freesurfer] Mapping Vertices from Subject to MNI using mri_label2label

It is hard to tell what is happening in that image, but it looks like the overlap is pretty close? One does not expect the overlap to be perfect, esp since the MNI152 is not a real subject. It would be easier to judge if you rendered the labels on the surface. On 05/31/2017 02:55 PM, Hengda H

Re: [Freesurfer] Contrast matrix format {Disarmed}

What p-values are you comparing to? You should run the analysis with mri_glmfit.m Are you sure that the design matrix is exactly the same in R? The design matrix in Xg.dat On 05/31/2017 02:10 PM, Hilton, Benjamin Taylor wrote: > > Sorry I don't think I've been very clear, got off on a tangent

Re: [Freesurfer] question about recon-all

You probably have cerebellum or some extra cerebral structure attached to the brain. Check the wm.mgz On 05/31/2017 02:15 PM, Jasmin Alves wrote: > Hello, > > I have used FS6.0 to do recon-all on about 57 brains, but for some > reason, recon-all is not working on some brains, recon-all is not

[Freesurfer] question about recon-all

Hello, I have used FS6.0 to do recon-all on about 57 brains, but for some reason, recon-all is not working on some brains, recon-all is not able to get past "Automatic topology fixer", after the command has been running for 24 hours. Is it possible there is too much motion in the image? Or does

Re: [Freesurfer] Contrast matrix format {Disarmed}

Sorry I don't think I've been very clear, got off on a tangent about the program before that sort of sidestepped the original question. We're running a linear regression in R with the individual values from the cache.th40.neg.y.ocn.dat file, with values of one cluster as the dependent variable

Re: [Freesurfer] label file from freesurfer 5.3

Thanks, Bruce! It works now. Is it possible I can convert all the negative values in the label to something like 1? Best, Daniel -- Y.J. Daniel Yang, Ph.D. Assistant Research Professor Autism and Neurodevelopmental Disorders Institute The George Washington University and Children’s National Hea

Re: [Freesurfer] label file from freesurfer 5.3

Hi Daniel it's because the values in your label are all negative and the default threshold is 0. Set it to -20 or something and you will see the label cheers Bruce On Wed, 31 May 2017, Daniel Yang wrote: Thank you. I just sent it to your mailbox. --  Y.J. Daniel Yang, Ph.D. Assistant Resea

Re: [Freesurfer] label file from freesurfer 5.3

Thank you. I just sent it to your mailbox. -- Y.J. Daniel Yang, Ph.D. Assistant Research Professor Autism and Neurodevelopmental Disorders Institute The George Washington University and Children’s National Health System E-mail: daniely...@gwu.edu > On May 31, 2017, at

Re: [Freesurfer] label file from freesurfer 5.3

sure, but I'll need the subject as well (at least one surface) On Wed, 31 May 2017, Daniel Yang wrote: Good to know, then, it must be the way I interact with FS 6.0.0 that is wrong. It’s a surface label. Can I send you the label file to see if you could view that in FS 6.0.0’s freeview using

Re: [Freesurfer] label file from freesurfer 5.3

Good to know, then, it must be the way I interact with FS 6.0.0 that is wrong. It’s a surface label. Can I send you the label file to see if you could view that in FS 6.0.0’s freeview using command line? -- Y.J. Daniel Yang, Ph.D. Assistant Research Professor Autism and Neurodevelopmental Dis

Re: [Freesurfer] label file from freesurfer 5.3

no, the label format should be backwards compatible. Was it a surface or volume label? On Wed, 31 May 2017, Daniel Yang wrote: Dear FreeSurfer experts, When I tried to use FreeSurfer 6.0.0’s freeview to open a label file generated by FreeSurfer 5.3, I could not see anything. Is it incompatib

[Freesurfer] label file from freesurfer 5.3

Dear FreeSurfer experts, When I tried to use FreeSurfer 6.0.0’s freeview to open a label file generated by FreeSurfer 5.3, I could not see anything. Is it incompatibility issue going on here? Thanks, Daniel ___ Freesurfer mailing list Freesurfer@nmr

Re: [Freesurfer] DIAG influencing recon-all pipeline?

That's really good to know. All machines are up and running. All of them use the same subject (OAS1_0001_MR1) from OASIS-Brains for analysis. I have a minimum archive of the current FreeSurfer 6.0.0 release, named "freesurfer-linux-x86_64-pipeline-6.0.0.tar.gz" (~ 400 MB) that is only capable t

Re: [Freesurfer] Multiple comparisons

Do you mean that you are doing an ROI analysis on the volume of the ROI? If so, then you still need to correct for multiple ROIs, probably with bonferroni or FDR. On 5/31/17 8:10 AM, Laura Ferrero Montes wrote: >Dear FS team, >I was doing a statistical analysis using metrics that are pr

Re: [Freesurfer] DIAG influencing recon-all pipeline?

Hi Jens we need more information if we are to help you. Can you send the recon-all.log? Or at least the bit that shows the command that fails onwards? The DIAG stuff should not change recon-all, but of course it might and if so we will track it down and fix it cheers Bruce p.s. The HIPS warn

[Freesurfer] Multiple comparisons

Dear FS team, I was doing a statistical analysis using metrics that are provided in stats files like volume of different regions, so I am not doing a voxel based morphometry. It is necessary to correct for multiple comparisons or as I am only comparing the measures of the regions betwe

[Freesurfer] Project volumes in MNI to lrsym_fsaverage6

Dear freesurfer experts I have processed resting state fMRI data in MNI space , for example: Data: 91*109*91*240, 240 was the time frames number. How could i project the data in MNI space to the symmetric surface(eg lrsym_fsaverage6) ? Thanks in advance! Meiling