[Freesurfer] Problems with FtpFileExchange

Dear FreeSurfer Developers, I am having problems with FtpFileExchange. I am trying to upload a compressed file Bruce asked me to upload and it seems I am missing something in the last point of the instructions: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange *What I have done till now*:

[Freesurfer] Back to native space after registration

Hi experts, Will you please briefly explain to me the rationale behind why subjects put back into their original space after alignment to the template (fsaverage)? and also, how this is done. Thanks so much, Avi CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for t

[Freesurfer] Tessellation: factors that could affect number and size of faces

Dear FreeSurfer experts, I have a question regarding the tessellation step, in which the surface is covered by a mesh of triangles. 1. How would the number/sizes of triangles be affected/ alter as a result of different brain volumes/sizes of different subjects? i.e. would a subject with a bigg

Re: [Freesurfer]  hippocampus subfields

Hi Bruce, There is aseg.stats. Is it brain segmentation volume? And in QDEC, I study the relationship between age and the cortical thickness, volume and surface area. The eTIV for volume and surface area should be set in Nuisance Factors, but for thickness, it's not need. Is right?

Re: [Freesurfer]  hippocampus subfields

no, eTIV is the estimated volume of the intracranial vault, so it included sulcal CSF. I think we include a whole brain volume in the aseg.stats file that you can use, although I don't remember what it's called cheers Bruce On Wed, 22 Nov 2017, 郑凤莲 wrote: Hi Bruce,     Thank you very much. I

Re: [Freesurfer]  hippocampus subfields

Hi Bruce, Thank you very much. I will try it. And I have another question. I also want to study the relation between age and the whole brain volume, gray matter volume and white matter volume. The whole brain volume is the same as eTIV, is right? Thanks, Zheng At 2017-11-22 10:29:4

Re: [Freesurfer]  hippocampus subfields

you would include it as a nuisance variable in the glm On Wed, 22 Nov 2017, 郑凤莲 wrote: Hi Bruce,      Thanks for your quick reply. These results are not correted by eTIV, If eTIV are corrected, I can only get the p value and scatter plot, I can't get the line trend. Do you know how to get t

Re: [Freesurfer]  hippocampus subfields

Hi Bruce, Thanks for your quick reply. These results are not correted by eTIV, If eTIV are corrected, I can only get the p value and scatter plot, I can't get the line trend. Do you know how to get the line trend with eTIV corrected as these results? Thanks, Zheng 在 2017-11-22

Re: [Freesurfer]  hippocampus subfields

is this eTIV corrected? I would look at some of the outliers and make sure that the segmentations are accurate. Certainly the trend is in the correct (and depressing) direction. cheers Bruce On Wed, 22 Nov 2017, 郑凤莲 wrote: Hi Bruce,     Thanks for your advice. There are a part of the result.

Re: [Freesurfer]  hippocampus subfields

Hi Bruce, Thanks for your advice. There are a part of the result. Blue color stands women, and Red color stands men. The number of the data is not enough large. Are they ok? May I use them in my paper? Thanks a lot ! Zheng At 2017-11-20 10:15:49, "Bruce Fischl" wrote: >Hi Z

Re: [Freesurfer] ERROR: fast_sexavg3() failed\n

Hi Freesurfer team, I am wondering if you received my last email which contained the log files you were asking me to send to you. Please let me know if you would like me to resend, Thank you very much. Best, Christina On 15.11.2017, at 15:22, Christina Pressl mailto:cpre...@rockefeller.edu>>

Re: [Freesurfer] Skullstrip commands not working

Hi Arsenije, -autorecon-pial should not recreate the brainmask. Is the brainmask.mgz currently correct? Bruce On Tue, 21 Nov 2017, Arsenije Subotic wrote: Dear experts, I recently finished processing a subject for whom I had performed a skullstrip on the brainmask volume. I decreased t

Re: [Freesurfer] Recon-all -hires

oh, this may be a version mismatch then. Which version of FS are you using? On Tue, 21 Nov 2017, Hwee Ling Lee wrote: Dear Bruce, Thanks for your reply. I checked the folder and did not find the file that was requested. What I have in the average folder that has 'RB*.gca' are 'RB_all_2016-05-

Re: [Freesurfer] T1 and brainmask wonky: Pieces of putamen missing

Hi Diana the subcortical segmentation only uses the brainmask as a binary in brain/out of brain mask to remove non-brain tissue. The intensities are irrelevant - only the intensities in the norm.mgz matter for the aseg. cheers Bruce On Tue, 21 Nov 2017, diana hobbs wrote: > > Update to my fi

Re: [Freesurfer] T1 and brainmask wonky: Pieces of putamen missing

Update to my first email: Hello again FS Developers and anyone experiencing the same problems, A colleague of mine has found what we think has already been addressed in the following link: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-November/048666.html >From the sounds of it,

[Freesurfer] Skullstrip commands not working

Dear experts, I recently finished processing a subject for whom I had performed a skullstrip on the brainmask volume. I decreased the watershed parameter and re-examined the brainmask and the portion of the skull was gone, although some dura was left over. I did a recon-all using the following

[Freesurfer] hippocampal subfields stats

Dear Freesurfer Developers, I’ve run the new longitudinal hippocampal subfields segmentation using Freesurfer’s developer version. Then I decided to extract stats for each hierarchy: HBT, FS60 and CA. I used the following command, for example: mri_segstats —seg lh.hippoAmygLabels-T1.long.v20.C

Re: [Freesurfer] Problems when loading surface and mesh showing vertices

Dear Bruce, I am using FileDropv2.0... I hope you and all the members of the list can access into this subject. Thank you for your help in advance, Rosalia 2017-11-21 18:35 GMT+01:00 Rosalia Dacosta Aguayo : > Sorry Bruce, > > Here is the problem I wanted to avoid: > > freesurfer-Lin

Re: [Freesurfer] Recon-all -hires

Dear Bruce, Thanks for your reply. I checked the folder and did not find the file that was requested. What I have in the average folder that has 'RB*.gca' are 'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'. The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.

Re: [Freesurfer] Problems when loading surface and mesh showing vertices

Sorry Bruce, I have sent it to your email directly...in order to avoid the process of uploading the data...because I am not familiar with it. Kind regards, Rosalia 2017-11-21 18:25 GMT+01:00 Rosalia Dacosta Aguayo : > Sorry Bruce, > > I prefer sending it to your email directly, then if you want

Re: [Freesurfer] Problems when loading surface and mesh showing vertices

tar and gzip the entire subject dir and upload it following these instructions: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Tue, 21 Nov 2017, Rosalia Dacosta Aguayo wrote:  Hi Bruce, Thank you for answering. Not, it is not a bug...in fact recon-all...-all had not problems

Re: [Freesurfer] Problems when loading surface and mesh showing vertices

Hi Bruce, Thank you for answering. Not, it is not a bug...in fact recon-all...-all had not problems. Just I was looking at the outputs...and as I am running FreeSurfer for my first time I wanted to ask about if this was a problem or I can go on Where I should upload the subject and which fi

Re: [Freesurfer] Problems when loading surface and mesh showing vertices

hmmm, that is odd looking. Can you upload that subject so we can see if it is just a display bug or not? On Tue, 21 Nov 2017, Rosalia Dacosta Aguayo wrote: > Dear FreeSurfer Developers, > > I am checking the OutputData_freeview after running recon-all following your > tutorial: > https://surfer

Re: [Freesurfer] Recon-all -hires

Hi Hweeling what is FREESURFER_HOME set to in the environment? Does that file exist? It is a standard part of our distribution cheers Bruce On Tue, 21 Nov 2017, Hwee Ling Lee wrote: > Dear all, > > I have T1 images collected from the 7T MRI scanner. > > I downloaded the most recent frees

[Freesurfer] Recon-all -hires

Dear all, I have T1 images collected from the 7T MRI scanner. I downloaded the most recent freesurfer software, and followed all instructions to install the software before using it. I would like to segment the T1 data using its high resolution image, and also to segment the hippocampal subfield

[Freesurfer] error in make_average_subject

Dear FreeSurfer Experts, I’m getting an error in make_average_subject and can’t find the reason. Please see the following for the error log from recon-all.log: Loading aseg from /gpfs/projects/RadImagSci/CFN/test-SDA-import/VTRAK4/xserveraids/vtrak4/mci/IMAGENE/NIFTI_CENTRAL/IMAGENE_BL_DENOISE

Re: [Freesurfer] fsaverage template appropriate to use with pediatric population?

Hi Avi we have found fsaverage to be fine in that age range, but if you are concerned you can use make_average_subject to build your own average. cheers Bruce On Tue, 21 Nov 2017, Avideh Gharehgazlou wrote: Hi experts, I have a few questions regarding the use of fsaverage template for my r

Re: [Freesurfer] cuda compile help

To close this thread, on centos7 'git annex' is an invalid command. That can be fixed with yum install epel-release yum install git-annex git-annex get --metadata fstags=makeinstall . Now the 'make install' finishes without errors. -Henk From: freesurfer-bo

Re: [Freesurfer] CSF mask with aparc+aseg

Hello again FS experts, Has anyone encounter this issue with FS CSF masks I described below? I’ve reposted the issue here. I appreciate the help! I am attempting to generate a CSF mask from my aparc+aseg.nii image file. However, my mask seems to only encompass the ventricular system itself, ignor

[Freesurfer] Problems after running recon-all ...-qcache

Dear FreeSurfer Developers, I have run recon-all-qcache after reviewing the recon-all...-all outputs in freeview. I have been looking into: https://surfer.nmr.mgh.harvard.edu/fswiki/mris_preproc Now it seems that I could have omitted the -qcache...and I am a bit lost with the examples sh

[Freesurfer] bash: /home/aimsl/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory

Hi, I'm a beginner of freesurfer, I was going through the tutorial step by step in Linux. After 'export FREESURFER_HOME=/usr/local/freesurfer' 1) 'source $FREESURFER_HOME/SetUpFreeSurfer.sh' the interface showed: FREESURFER_HOME/home/aimsl/freesurfer FSFAST_HOME /home/aimsl/frees