Freesurfer June 2022

freesurfer@nmr.mgh.harvard.edu

84 participants
123 discussions

HRF with derivatives: results
by Laura Doll 09 Jun '22

09 Jun '22

External Email - Use Caution Hi everyone, I need some help regarding the SPM-HRF with two derivatives: Where can I find the actual function that was used for the analysis? I am mostly interested in the peak latency, but would also appreciate if I can check the other parameters of the function somewhere. Best, Laura

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creating. or replacing a label of choice in aseg atlas
by Ramtilak Gattu 09 Jun '22

09 Jun '22

External Email - Use Caution Hi, We are interested in replacing a couple of labels in aseg atlas with our own roi's already in the same space as of "aseg.mgz" atlas in the fsaverage folder. What would be the best way to do this? Could someone help or guide me if anyone has done something similar to this query? Can I just add the regions (in the form of 3d masks) to the aseg atlas and create aseg_modified.mgz and later replace the aseg.mgz with aseg_modified.gz and rename the aseg_modified.mgz back to aseg.mgz. If I follow this procedure and run "recon-all" will the aseg_stats will give me volumes based on the new volumes? -- Regards Tilak

2 5

surface based analysis using Infant FS
by Steger Celine 09 Jun '22

09 Jun '22

External Email - Use Caution Dear FS experts, We are currently exploring the Infant Freesurfer pipeline for surface based analysis in our cohort. The generated surfaces seem reasonable, but now we are wondering, how to proceed. To our understanding, by looking at the recon-all for adult data, the next step would be to register each subject to standard space (using the -qcache flag this happens directly to fsaverage). Since the -qcache flag is not available in infant_recon_all we would like to clarify if this is not advised to do so with subjects processed via infant_recon_all or if we could just proceed with recon_all from here. Is there is any alternative procedure that should be followed in order to map all subjects into one space, e.g. creating a cohort specific average? Kind regards, Céline

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Password to unzip the FreeSurfer image
by Dokumaci, Ayse Sila 09 Jun '22

09 Jun '22

External Email - Use Caution Hello, I was wondering if I could get the password to unzip the FreeSurfer image for Virtual Box running on Windows? I thought this would not be publicly available on the archive. Kind Regards, Sila

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Fwd: PET postdoc at NIH
by Douglas N. Greve 08 Jun '22

08 Jun '22

-------- Forwarded Message -------- Subject: PET postdoc at NIH Date: Wed, 8 Jun 2022 19:44:38 +0000 From: Innis, Robert (NIH/NIMH) [E] <innisr(a)mail.nih.gov> To: Innis, Robert (NIH/NIMH) [E] <innisr(a)mail.nih.gov> External Email - Use Caution A postdoctoral position will be available in my lab starting in late 2022 or early 2023. Please forward the attached advertisement to anyone who may be interested. Although immodest of me to say, the lab’s research projects are at a very exciting and productive stage. The two major goals are translational studies of neuroinflammation (i.e., COX-1, COX-2, and TSPO) and indirect markers of cAMP signaling (via PDE4B and PDE4D). The studies extend from transgenic mice to monkeys and to patients, including those with depression or dementia. Stay safe and many thanks, Bob Innis ************************************ Robert B. Innis, MD, PhD Chief, Molecular Imaging Branch National Institute of Mental Health 10 Center Drive, MSC-1026 Bldg. 10, Rm. B1D43 Bethesda, MD 20892-1026 Tel: 301-594-1368 Fax: 301-480-3610 Email: robert.innis(a)nih.gov <mailto:robert.innis@nih.gov> Branch Administrative Manager: Elizabeth Alzona Tel: 301-594-1089 Email: alzonae(a)irp.nimh.nih.gov <mailto:alzonae@irp.nimh.nih.gov> Molecular Imaging Branch website<https://secure-web.cisco.com/13uSddekZGczNs04Fv2mZOPapEbeQA6rUbBr1C7X4wwVZj…> ************************************ ____________________________________ LEGAL CONFIDENTIALITY NOTICE: This email message (including all attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.

1 0

Password request
by Catarina Duarte 08 Jun '22

08 Jun '22

External Email - Use Caution Hello, I am writing to request the password to unzip the Freesurfer 7 image (for VirtualBox running on windows). I appreciate your help. Best, Catarina Duarte

1 0

instalation
by refaat el-said 07 Jun '22

07 Jun '22

External Email - Use Caution Good eveningI downloaded Freesurfer 7.2.0 release in Ubuntu 18.04.06: FS_7_2_0_Ubuntu_18_04_06.ova.7zCan you please send me the password to open the zip file?Refaat

1 0

vertex ID in the contralateral hemisphere
by Marina Fernández 07 Jun '22

07 Jun '22

External Email - Use Caution Dear experts, I would like to know the corresponding vertex in the contralateral hemisphere of a given vertex. Do you have a function that allows me to know it? Thank you very much in advance. Best regards, Marina

2 1

VM Image Passcode
by Victoria Jones 07 Jun '22

07 Jun '22

External Email - Use Caution Hello, I've downloaded the VM image (FS_7_2_0_ubuntu_18_04_06.ova.7z) and need the passcode to expand it. Thank you! Best, Victoria -- *Victoria Jones* *(she/her or they/them)* Doctoral Candidate Department of Chemical Engineering & Materials Science University of Minnesota 717-926-7312

1 0

Custom LUT
by Benjamin Deck 07 Jun '22

07 Jun '22

External Email - Use Caution Responding re: Douglas Greve How exactly did you create the LUT? Eg, in windows using notepad? I'm thinking that there might be some hidden characters in there as the color is wrong. I did notice that your first entry had a value of 5 in the last column; usually this is 0 (not sure what it is for). What happens if you switch the LUT to the default? Do you get reasonable colors (even if the names are wrong)? Reply: I used a custom python script that creates a LUT for each subject. Then I ran dos2unix to ensure the line endings were appropriate. If I load the default FS LUT only 2 ROIs are being labeled. Does this mean that I have an issue with my mri_concat call? Which is: mri_concat --sum --f vols.txt --o sub_vols.mgz Thanks, Ben -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/1orR-DWFSm7AzAYYcqvCSHmblQoGORO7YzkKJqo0iTu7-y…> Virus-free. http://secure-web.cisco.com/1y12Z5EuR0Thcv3zHQ2WDObPbPtIi3GheXNDJxePf3Sumjp… <https://secure-web.cisco.com/1Q_PewrE8ioL4nGaDXS3HygbqgAIyt7ilGvMJtVbT_Yof-…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Freesurfer June 2022