Freesurfer May 2016

freesurfer@nmr.mgh.harvard.edu

135 participants
197 discussions

Segmentation of deskulled volume
by Aquino Domenico 26 May '16

26 May '16

Dear Freesurfer team, I'm trying to segment a brain from a non standard sequence. It is a 3D IR sequence that I have previously pre-elaborated and deskulled. The software is running from a long time and at the moment is correcting defects (17/128) but I'm not sure it's working properly. I'm sending you the volume in NIFTI_GZ format. Could you please help me in detecting some possible issues? Thanks a lot, Domenico

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recon-all on 0.5mm scan?
by Trisanna Sprung-Much 26 May '16

26 May '16

Hi Freesurfer I would like to know if it is possible to create surfaces from a scan that is 0.5mm isotropic. I tried to run recon-all on our MNI 2009b atlas which is 0.5mm cubed and it crashed quite quickly afterwards. I wonder if this has to do with the fact that Freesurfer tried to conform it to 1mm isotropic? When I ran recon-all on the 1mm atlas it created some nice surfaces. Let me know if you would like the .log as I cannot seem to make much sense of it. best wishes Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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Rat model in FreeSurfer
by Melanie Ganz 26 May '16

26 May '16

Hi, one of our lab mates who works with small animal models would also like to try FreeSurfer. I know from the mail archive that people have used it like this before. Could any people that have used it on rats please give some info on what they have tried? Cheers, Melanie -- Melanie Ganz-Benjaminsen, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark phone: +45 3545 6718 e-mail: Melanie.Ganz(a)nru.dk web: http://melanie.clausundmelanie.de/

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surfaces from 0.5mm scan
by Trisanna Sprung-Much 25 May '16

25 May '16

Hi there My initial email didn't seem to have sent and so I am re-sending it: I would like to know if it is possible to create surfaces from a scan that is 0.5mm isotropic. I tried to run recon-all on our MNI 2009b atlas which is 0.5mm cubed and it crashed quite quickly afterwards. I wonder if this has to do with the fact that Freesurfer tried to conform it to 1mm isotropic? When I ran recon-all on the 1mm atlas it created some nice surfaces. Let me know if you would like the .log as I cannot seem to make much sense of it. best wishes Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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Need Help
by HARI GURAGAIN 25 May '16

25 May '16

Hello, I am kind of new to the neuroimaging. I was trying to reproduce the following type of figure in freesurfer (3d image with thickness). But I couldn’t do that. Is it possible for anyone to explain how to generate such figure from mri data. Just to clarify, I have the mri data in the form of *.dcm. Is there any specific command to get through it? I tried to work on similar figures using tksurfer *** but couldn’t produce. Your help is greatly appreciated. Thank you, Hari This figure is from one paper. Fig. 4. 3D models of the pial surfaces generated by FreeSurfer with a colored overlay of the local cortical thickness in mm. The top row shows the pial surfaces of the left and right hemisphere based on data with an isotropic resolution of 0.5 mm and the bottom row with an isotropic resolution of 1 mm; both data sets have been acquired at 7 T.

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White matter segmentation
by Mahmoudi, Fariborz 25 May '16

25 May '16

Dear All, I want to segment white matter into 131xx and 141xx label series. I used aparc.a2009s but it just gave me cortex labels (111xx and 121xx). Can anyone guide me how could I do this? Regards, Fari ________________________________ CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies. Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy & Security page on www.henryford.com for more detailed information as well as information concerning MyChart, our new patient portal. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.

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Tract length
by Alan Francis 25 May '16

25 May '16

Hi Imagers - I am looking at the Uncinate fasciculus in a Cannabis use disorder (CUD). I found that CUD subjects have significantly shorter tract length and a significant group x side interaction in comparison with controls. Have you seen this before? What is the interpretation of this finding? Thank you, Alan

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FreeSurfer 5.3 OASIS
by Gouveia, Vítor 25 May '16

25 May '16

Hello, I've been trying to process a subject from the OASIS database with FreeSurfer 5.3. FS is relative new to me. I'm trying to use recon-all with -all but the format img/hdr does not seem supported. Do you have any ideia what should I do to process these images? Thank you. Sincerely, Vitor

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DTI error
by Jasmin Alves 25 May '16

25 May '16

Dear Freesurfer, While doing the bedpost step for TRAC-all ( trac-all -bedp -c dmrirc1_sim.txt) I received the following error: /Applications/freesurfer/bin/bedpostx_mgh: line 345: kill: (51042) - No such process Any ideas? Thank you, Jasmin Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

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Improve normalization with own average subject
by pfannmoelj＠uni-greifswald.de 25 May '16

25 May '16

Dear Experts, I am currently working with the non-linear FreeSurfer normalization. We have a small group of subjects N = 12 and in each brain we identified a single position with a fMRI localizer. The task is a group comparison of the individual results for this position. Therefore, the coordinates of each position in FSaverage was determined using mri_label2label. The radius of the region is an important quantity in my investigations. A smaller radius would help me a lot in my data processing. I tried to decrease the radius by generating a new group space template from my 12 subjects with make_average_subject. Then I used mri_label2label to determine the coordinates in the new group space template. Unfortunately, there was no difference in the radius. The intention behind this procedure was to achieve an improved normalization of the subjects. I have read much about this topic in the mailing list, but there are many details in the processing which I am not yet aware of. So, my question is if I proceeded the best possible way or if there is a better alternative to improve the normalization. Would it help to generate a new template as outlined in the second part on this web tutorial (chapter: Creating a registration template from scratch): https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates or do I need to use mris_register with my new template and my 12 subjects instead of mri_label2label in order to benfit from my new template as generated by make_average_subject (also outlined in the web tutorial in the chapter: Creating a registration template initialized with FreeSurfer template)? Even a small decrease in the radius would help to improve my results. Thanks in advance pfannmoe

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Freesurfer May 2016