Freesurfer

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30133 discussions

FLAIR T1 misregistration
by Robert Kraft 16 Dec '16

16 Dec '16

I am trying to run recon-all with a T1w image and a FLAIR image to improve the removal of the dura. I am using the command recon-all -sd /cenc/mri/freesurfer -subjid 34P1001 -all -i /cenc/mri/subjects/34P1001/freesurfer/input/t1w.nii.gz -FLAIR /cenc/mri/subjects/34P1001/freesurfer/input/t2flair.nii.gz -FLAIRpial I have two questions. First, in reading the forums I read several threads on the forum saying that you run the recon-all without the -FLAIRpial option and then run recon-all -autorecon3 -s $SUBJECT -FLAIRpial — (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28033.html) Is it necessary to run -autorecon3 with -FLAIRpial option after recon-all has been run with the T1w image? It seems that if the -FLAIRpial option only is needed in -autorecon3 then it should be able to be specified simultaneously. I did try it the way posted with similar results for some images. My biggest concern is that there is a severe misregistration between my T1w image and my FLAIR image. What can I do to improve the registration? The raw data are almost perfectly aligned (i.e. the subject did not move between acquisitions) so this misregistration has me baffled.. After registration the FLAIR image has been shifted and rotated. There is also a hyper intensity shading on the superior brain regions (best seen in the sagittal view). I have posted the mri and scripts folder to Google Drive if anyone cares to take a look https://drive.google.com/drive/folders/0B4bmIh8K5WVJbDRpNXh1TVEzdVU?usp=sha… I have also included 3 screen shots showing the issue of misregistration and hyper intensities. Any suggestions on how to resolve this issue would be greatly appreciated. Thanks for your help in advance Bob

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Re: [Freesurfer] how to make label from volumetric mask? (Douglas N Greve)
by Niia Nikolova 16 Dec '16

16 Dec '16

Thank you, that worked perfectly!

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6.0 release date?
by Vaz pandolfo, Renata 16 Dec '16

16 Dec '16

Dear FS experts, My colleagues and I are planning some projects and we were wondering if there are any news on the release date of the FreeSurfer 6.0 stable version. We noticed that there was a new developmental version released today, is that good news? An approximation of whether it will be a matter of weeks or months would suffice. Thank you! Renata

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questions about registration tool in Freesurfer
by Frank Robert 15 Dec '16

15 Dec '16

Dear FS experts I want to use Freesurfer registration tools. I check https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommandsRegistration?hi… 1). Here it is the term " modality" I want to get clarification. It is easy to know Modality is different between CT, MRI and PET. But if MRI use different sequence, T1, T2, DWI, ASL to get different images, it is the same modality or different modality? 2). mri_coreg is strongly recommended for use. But I can not find the instruction in Wiki. 3.) If I register ASL source image and subtraction images to T1w images, I guess that preciseness of registration will be higher if use source images to register. Is it right? If it is correct, If I use ASL source images to register to get .lta file, how can I apply .lta file to apply for subtraction images? Do you have instruction? Many thanks Best Regards Frank Yu

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(no subject)
by Sadhana Singh 15 Dec '16

15 Dec '16

Hi I am using freesurfer for calculation cortical thickness in my subjects. Firstly, I have converted all the T1 weighted images from dcm into nii.gz format. After that, I have run the recon-all in one subject using this script 'recon-all -i CON_101.nii -s CON_101 -all' , but it shows error The error is: [kumarlab@lcmodel ~]$ cd /home/kumarlab/Downloads/ Freesurfer_VBM [kumarlab@lcmodel Freesurfer_VBM]$ export SUBJECTS_DIR=/home/kumarlab/ Downloads/Freesurfer_VBM [kumarlab@lcmodel Freesurfer_VBM]$ recon-all -i CON_101.nii -s CON_101 -all ERROR: cannot find CON_101.nii Linux lcmodel 3.10.0-327.el7.x86_64 #1 SMP Thu Oct 29 17:29:29 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Thu Dec 15 16:14:29 EST 2016 Regards *Sadhana Singh, PhD *

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mri_coreg question
by Frank Robert 15 Dec '16

15 Dec '16

Hello FS experts I followed the instruction to download the mri_coreg file from website https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg put it on my virtual machine ubuntu \local\user\freesurfer\bin directory. But I run it and it say <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg> \local\user\freesurfer\bin\mri_coreg can not execute binary file? I use sudo chmod u+x mri_coreg to make it executable. Do you know why? Frank Yu Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Oct 3 to freesurfer you can get it from here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg On 10/03/2016 12:46 PM, Hsin-Tsung Lee wrote: > Dear Dr. Bruce > I have one more question, does the "mri_coreg" available in > version 5.30 stable, or it only available in v6.0(or it's beta version)? > > Best Regard

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Infant brain atlas
by Axelson, Eric D 15 Dec '16

15 Dec '16

I asked this last week with no response: Does the infant brain atlas mentioned in this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/ exist yet or will it be included in version 6? Thanks Eric Axelson Research Specialist Department of Psychiatry University of Iowa eric-axelson(a)uiowa.edu<mailto:eric-axelson@uiowa.edu> ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

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how to make label from volumetric mask?
by Niia Nikolova 15 Dec '16

15 Dec '16

Dear Freesurfers, I have some binary ROI masks of MT/V5 that I’ve drawn from activation maps in fslview, which I would like to transform into labels so that I can project them onto a surface and flat patch. I have been following parts of this thread https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32468.html <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32468.html> and have tried using mri_vol2surf and mri_cor2label, but I cannot view the result either with tksurfer or freeview. I would like to be able to load the subjects inflated surface with tksurfer, and add the mask as a label, or something similar. The commands I’ve used are as follows: mri_vol2surf —src MST_L_bin.nii.gz —out MST_L_surf.mgh —out_type mgh —hemi lh —srcreg MST_L_to_BGimage.dat —projdist 0.5 —ref MST_L_bin.nii.gz mri_cor2label —i MST_L_surf.mgh --id 1 —l lh.mst.label I previously created MST_L_to_BGimage using fslregister. I am also attaching the input mask file as well as the label file that I generated in this way. Are these the right programs to use in this case, and if so, what is the appropriate way of using them? Thank you in advance for any help. Sincerely, Niia

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problem of using freesurfer
by Hsin-Tsung Lee 15 Dec '16

15 Dec '16

Dear freesurfer community I have used the freesurfer v5.30 stable on linux, I want to fusion the CT image and the MRI T1 image. The CT image was signed form the epilepsy patient after the inserted depth electrode surgery. The MR image was sign before the operation. I tried to register them by the "bbregister" or "mri_robust_register" , but it didn't work good. And I had seen the website page " https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-June/046081.html" , does the "mri_coreg" is the better instruction to use in my case? And, I found that I can't find the download link of freesurfer v6.0 in your website, and the link " ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg.mac " is invalid to use. I really appreciate any help here HsinTsung Lee

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incorrect pial surfaces after watershed adjustment
by Rizvi, Batool 15 Dec '16

15 Dec '16

Hi FreeSurfer experts, We have a subject on which we had to do adjust the watershed parameters for, since there was some brain missing from the brainmask.mgz. The watershed itself worked, but after that, we needed to regenerate the surfaces after the bad skull strip was fixed, and we ran "recon-all -autorecon-pial -subjid <subject name>" That seemed to not work though, and it still shows that the surfaces do not include the new brain matter. Attached is an image of the output. Is there anything else we can try to regenerate these surfaces correctly? Thank you! Batool

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