Re: [Freesurfer] contrast

Thank you very much again Dough, I was hoping that i understood how to make a contrast! Thank you! To: freesurfer@nmr.mgh.harvard.edu From: gr...@nmr.mgh.harvard.edu Date: Thu, 9 Jun 2016 22:10:04 -0400 Subject: Re: [Freesurfer] contrast I responded in the body of the email

Re: [Freesurfer] contrast

I responded in the body of the email On 6/9/16 7:57 PM, Dave Yas wrote: /*Helllo! That was an empty email! */ > To: freesurfer@nmr.mgh.harvard.edu > From: gr...@nmr.mgh.harvard.edu > Date: Thu, 9 Jun 2016 16:33:48 -0400 > Subject: Re: [Freesurfer] contrast > > > > On 06/08/2016 11:40 PM, Dave

[Freesurfer] wm.mgz edits amygdala hippocampus cerebral cortex

Dear all Freesurfer users, I have a few questions regarding wm.mgz edits. I am very new to this area and have only recently started using Freesurfer so please excuse me if my questions appear naive or misinformed. I have managed to make most of the necessary edits needed to fix skullstrip

Re: [Freesurfer] contrast

Helllo! That was an empty email! > To: freesurfer@nmr.mgh.harvard.edu > From: gr...@nmr.mgh.harvard.edu > Date: Thu, 9 Jun 2016 16:33:48 -0400 > Subject: Re: [Freesurfer] contrast > > > > On 06/08/2016 11:40 PM, Dave Yas wrote: > > Thank you very much Dough! > > > > I need to check 4

Re: [Freesurfer] Coregister the CT image and MRI image

Dear Douglas, I have used the same file as you pointed, but it keeps on showing the same error message. I copied the file to my /Applications/freesurfer/bin directory but it still shows the same error message: >> ‘dyld: Library not loaded: @executable_path/../lib/gcc/lib/libgomp.1.dylib’ >>

Re: [Freesurfer] Coregister the CT image and MRI image

try ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg.mac On 06/09/2016 06:21 PM, HARI GURAGAIN wrote: > Dear Douglas, > > The executable is not working as it says ‘Library not loaded: > @executable_path/../lib/gcc/lib/libgomp.1.dylib’ > Referenced from:

Re: [Freesurfer] Coregister the CT image and MRI image

Dear Douglas, The executable is not working as it says ‘Library not loaded: @executable_path/../lib/gcc/lib/libgomp.1.dylib’ Referenced from: /Applications/freesurfer/bin/mri_coreg.mac Reason: image not found Trace/BPT trap:5 I am currently using the freeview: Version 1.0 and the operating

Re: [Freesurfer] converting ME-MPRAGE files

That tells you there is one "series" in that folder. The series here means a volume, though there are many dicom files. dicomdir/mr_0006-e02/3d_t1_memprage-00533.dcm is just one in the series. To use this, you can run recon-all -s yoursubject -all -i

Re: [Freesurfer] Coregister the CT image and MRI image

No, it is not the same command line. If you run it without args, it will give you some info, but it is basically mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta On 06/09/2016 05:22 PM, HARI GURAGAIN wrote: > Thank you Douglas. > One more thing: Is there any syntax how to use it? I

Re: [Freesurfer] Resampling the parametric map of brain activations onto a surface

Thanks again. I will follow the new instructions! Yue From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve Sent: Thursday, June 09, 2016 4:10:17 PM To:

Re: [Freesurfer] Coregister the CT image and MRI image

Thank you Douglas. One more thing: Is there any syntax how to use it? I wonder if it is same as the mri_robust_register? > On Jun 9, 2016, at 3:43 PM, Douglas N Greve wrote: > > I don't think robust register will do cross-modal. You may be better off > using

Re: [Freesurfer] mri_binarize --rmax option unknown

Thanks very much, Doug! That version works perfectly. Just out of curiosity now, is there potentially a way to create a binarized mask in the other way that I mentioned? That is, to generate a mask that cuts maintains the middle 95% of the data (i.e. +- 2SDs of the signal mean) as a way to

Re: [Freesurfer] Command to summarize 35 cortical thickness

try aparcstats2table On 06/09/2016 05:09 PM, shi yao wang wrote: > Dear FS expert, > I am using command "mris_anatomical_stats -a > subjid/label/lh.aparc.annot -b subjid lh" to calculate cortical > thickness in 35 regions. > I have 50 subjects. I am wondering how can I summarize these results

[Freesurfer] converting ME-MPRAGE files

Hello All, We have acquired our anatomical images on a Siemens scanner as multiecho MPRAGE sequence (4 echos), and wish to unpack the runs so we can perform morphometric analysis using FreeSurfer. What is the optimal way to convert the DICOM files so we can use them with FreeSurfer tools?

Re: [Freesurfer] Resampling the parametric map of brain activations onto a surface

That one is out of date; we'll delete it. Thanks for pointing it out and sorry for our wiki pointing you in the wrong direction. We're in the process of weeding it out... On 06/09/2016 04:54 PM, Zhao, Yue wrote: > Hi Douglas, > > This is the instruction I am using. >

[Freesurfer] Command to summarize 35 cortical thickness

Dear FS expert, I am using command "mris_anatomical_stats -a subjid/label/lh.aparc.annot -b subjid lh" to calculate cortical thickness in 35 regions. I have 50 subjects. I am wondering how can I summarize these results and export to one document? (I just need cortical thickness results) thanks

Re: [Freesurfer] Resampling the parametric map of brain activations onto a surface

Hi Douglas, This is the instruction I am using. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FuncOverlay I cannot insert the picture in this email. I attach it. Hope it helps. Thanks very much! Yue From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Hi Eugenio, Would it also be possible to use the -hires flag in the initial recon-all command to prevent the T1 from being downsampled and maintain the voxel size that the T1 was acquired at, and use that resulting recon for the hippocampal subfield segmentation? I've tested this with MEMPRAGE

Re: [Freesurfer] mri_binarize --rmax option unknown

That was a bug which I have not fixed. Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize On 06/09/2016 03:53 PM, Lakhani, Bimal wrote: > Good afternoon, > > I am trying to run a fairly simple mri_binarize command on FS v 5.3, > Linux 64bit, but when I use

Re: [Freesurfer] Coregister the CT image and MRI image

I don't think robust register will do cross-modal. You may be better off using mri_coreg, which you can get from here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg On 06/09/2016 01:58 PM, HARI GURAGAIN wrote: > Dear Freesurfer community, > > I am relatively new to

Re: [Freesurfer] Resampling the parametric map of brain activations onto a surface

Sorry for the delay. I can't see the image. Also, what instructions are you following? They look pretty old. check out our multimodal tutorial instead https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview On 06/09/2016 10:19 AM, Zhao, Yue wrote: > > Hi All, > > > I am not

Re: [Freesurfer] Regarding: Surface projection of WMHs volume

You could create a label of the WMH (mri_cor2label), then use mri_label2label to map it on to the surface with the --paint option (run it with --help to see an example) On 06/09/2016 09:07 AM, Dr Sampada Sinha wrote: > Dear freesurfer expert, > > I don't know if this question make any sense but

Re: [Freesurfer] contrast

On 06/08/2016 11:40 PM, Dave Yas wrote: > Thank you very much Dough! > > I need to check 4 contrasts. I made them based on the freesurfer page, > but cant decide if i interpreted them right! > Are my contrasts Ok? > > If classes are: > Patients, healthy control > > and variables are: > Age,

Re: [Freesurfer] mri_binarize --rmax option unknown

Alternatively, is there another way to calculate the binzarized threshold min and max based on multiples of the standard deviation of the global mean? Thanks! On June 9, 2016 at 12:54:25 PM, Lakhani, Bimal (bimal.lakh...@ubc.ca) wrote: Good afternoon, I am

[Freesurfer] mri_binarize --rmax option unknown

Good afternoon, I am trying to run a fairly simple mri_binarize command on FS v 5.3, Linux 64bit, but when I use the option — rmax, I am getting an error that says the —rmax option is not recognized. It is made weirded because —rmin works perfectly. Here is the command line and the following

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Hi Eugenio, Did you already do this? If so, a published reference would be more useful to me than instructions for how to do it, as I¹m more interested in making an argument for an acquisition protocol modification. Matt. From: on behalf of "Iglesias,

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Hi Matt, you can use strategy 3 of my previous email ;-) Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 9 Jun 2016, at 19:31, Matt Glasser > wrote: I

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Hi Fernando, Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield code assumes that the T1 comes from FreeSurfer… For the paper, I hacked the code to take advantage of multiple images with higher resolution, but it hasn’t been thoroughly tested and it’s not publicly

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

I would be interested to know how well 0.7mm isotropic resolution data performs at hippocampal segmentation. It would be better if folks could do this then needing to acquire specialized anisotropic scans for hippocampal segmentation. Peace, Matt. From:

[Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Dear, I have a doubt regarding the input T1 image used for the Hippocampal Subfield segmentation in Freesurfer 6.0 - https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields In this documentation it says that I can use a standard 1mm T1 image or the same standard 1mm T1 image with an

Re: [Freesurfer] Symmetric label on fsaverage

Hello, Sorry for my late reply but I just tried these commands today. In fact, I don't have mris_left_right_register on Freesurfer 5.3 so I used this one : https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/ and it seems to work. Concerning mris_apply_reg, I am not sure how to

[Freesurfer] Coregister the CT image and MRI image

Dear Freesurfer community, I am relatively new to this community. I was trying to register the CT image and the MRI images (MRI as a the target volume and CT as the movable volume). I used the mri_robust_register to to do the registration as below: mri_robust_register --mov vol1.nii --dst

[Freesurfer] Segmentation Fault with mri_convert

I'm trying to convert the dicom to the original 001.mgz file using the following command on a Mac OSX Yosemite version 10.10.5. My SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/ . My current working directory is /Users/csfinuf/Desktop/freesurfer/morerepeat/ . The following

Re: [Freesurfer] Resampling the parametric map of brain activations onto a surface

Hi All, I am not sure if the question is successfully posted. If the post is there, does anyone has any idea? Thanks a lot! Yue From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Zhao, Yue

Re: [Freesurfer] Longitudinal Studies Question

Hi Carolyn, from you longitudinal qdec table you can create one that qdec can use by simply manually concatenating the first two collumns with a ".long." in the middle tpid.long.baseid and call that column "fsid" in the first row. This will instruct qdec to load the data from the

Re: [Freesurfer] tutorial data

Hi Everyone, I have found a solution and wanted to update this thread in case anyone runs into the same problem. I was able to download the tutorial data directly from this link: http://ftp.nmr.mgh.harvard.edu/pub/data/ - Arkadiy On Wed, Jun 8, 2016 at 7:44 PM, Arkadiy Maksimovskiy

[Freesurfer] Regarding: Surface projection of WMHs volume

Dear freesurfer expert, I don't know if this question make any sense but is there a way to project white matter hypointensities volume onto the surface? Thanks and kind regards, Sampada -- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical

Re: [Freesurfer] Brainmask edit error

Hi Sabrina, I talked to Bruce and he said we can improve the surfaces further if we try labeling the lesion as "Left_Lesion" in the aseg and then running recon-all from that point onward. It should freeze the white surface exactly where you draw voxels (so be careful with it) but still let