Freesurfer March 2022

freesurfer@nmr.mgh.harvard.edu

86 participants
124 discussions

Unit of the Numbers in cache.th40.neg.y.ocn.dat
by Na, Xiaoxu 17 Feb '24

17 Feb '24

External Email - Use Caution Dear Freesurfer Experts, As I'd like to extract the average value of each subject in the cluster after running group analysis, may I know the unit of these numbers? Since the one I'm running is surface area, and the cluster is 444mm^2, all the numbers in the file cache.th40.neg.y.ocn.dat is in the range of [0.55 1.05], may I know if this is correct and if so, how the unit is for those? Thanks a lot! ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx 1 -4.8321 40067 444.11 -58.1 -16.6 -23.9 0.0002 0 0.0004 670 -2784.11 Regards, Xiaoxu ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Reliability and sensitivity of two whole-brain segmentation approaches − ASEG and SAMSEG
by Donatas Sederevicius 28 Aug '22

28 Aug '22

External Email - Use Caution A new pre-print paper comparing two FreeSurfer’s whole-brain segmentation methods - ASEG and SAMSEG is now available (see the link below). The study is of great interest to many researchers in the field, providing new insights and guiding the selection of the processing method. https://www.biorxiv.org/content/10.1101/2020.10.13.335737v1

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SAMSEG and statistics
by k3ops＠free.fr 27 Aug '22

27 Aug '22

External Email - Use Caution Hi FreeSurfer community, I recently discovered the SAMSEG application in the FreeSurfer 7.2.0 release and started to give a try on few subjects were FreeSurfer was having a hard time to segment brain structures (due to poor contrast). So I have few questions to harmonize the SAMSEG and FreeSurfer statistical files: 1. "samseg.stats" file is not compliant with the "asegstats2table" application so I was not able to generate a final CSV file with volumetric results Is there another solution? 2. "samseg.stats" file does not provide large brain structures like "BrainSegNotVent" or "SupraTentorialNotVent", is there a way to get them calculated? 3. "samseg.stats" file does not provide left/right or global cortical thickness, is there a command line to execute to get these extra values? Thanks. Best, Florent

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Curvature data question
by Samuel Paré 05 May '22

05 May '22

External Email - Use Caution Hello, We are looking at some of our data acquired on a 7T magnet. We ran recon-all with the “highres” flag. The obtained results for cortical thickness and cortical volume are very comparable to data that we obtain when using 3 T brain images. However, the results for cortical curvature are significantly different from what we get by our 3 T data. I attach the output of mean cortical curvature values using the Destrieux atlas for a 3T and 7T dataset on healthy controls. As you can notice, they differ roughly by a factor of 2. Any explanation for what may cause this large difference? Thanks, Samuel [image: image.png] -- *Samuel Paré, MSc* Laboratoire du développement et plasticité du système visuel École d'optométrie Université de Montréal

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Paracingulate
by Roxanna Korologou-Linden 27 Apr '22

27 Apr '22

External Email - Use Caution Hi, I have been reading papers referring to the paracingulate cortex. What does this correspond to in the Desikan-Killiany atlas used in FreeSurfer? I am trying to compare my results to previous studies. I would appreciate your insight. Thanks, Roxanna

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Advice: changing Freeview light source?
by Sam Buck Johnson 08 Apr '22

08 Apr '22

External Email - Use Caution Dear Freesurfer Community, I use Freeview to render 3D views of overlays on cortical surfaces. For my current processing, the absolute scale of the overlay map is important, and this absolute scale is distorted / marred by the shading that Freeview adds due to its default light source. (E.g., the top of the image is lighter than the bottom.) My question is this: is there any way to change the default light source of Freeview? I would prefer to use a uniform ambient light that did not cast any shadow, such that each pixel’s rendered intensity was exactly correlated with the absolute value of the visualized overlay in that pixel. If this is not possible, a point light source “at infinity” pointing directly into the plane of view might also suffice, since I believe it would produce a uniform illumination on a spherical base hemisphere. (I could be wrong here.) One final note: ideally this method would be possible to achieve by the command line, or failing that, to manually change in the GUI such that the setting would be preserved upon quitting and restarting Freeview. As always, any help is much appreciated. If someone happens to know that this functionality is absolutely not available, I would certainly like to know that, too. Thanks in advance. Sincerely, Sam Johnson Postdoctoral Scholar Brain and Education Lab, Stanford University GSE

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Tkregister2 not opening GUI
by Isabelle Deschamps 04 Apr '22

04 Apr '22

External Email - Use Caution Good afternoon, I am trying to verify the registration and for some reason the GUI is not opening. I am using a Macbook Pro running macOS Montery with a 2.4 Gz Quad-Core Intel Core i5 I have Freesurfer version: maOS-7.2.0 I do not get an error when I run TKregister2 or TKregister_cmld This is the output that I get without the GUI opening No target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 0 ZeroCRAS 1 7.2.0 Diagnostic Level -1 % % % % % % % % avi2talxfm talairach.xfm --------------------- 1.00857 0.02020 -0.00990 -0.12365; -0.01789 1.03251 0.24795 -28.10577; 0.02556 -0.30660 1.20913 3.54973; 0.00000 0.00000 0.00000 1.00000; INFO: loading target /Volumes/RestingState/fMRI/fMRI/Freesurfer/S0010_FS/mri/orig.mgz Zeroing CRAS of target new xfm ----------------- 1.00857 0.02020 -0.00990 1.93629; -0.01789 1.03251 0.24795 -11.46406; 0.02556 -0.30660 1.20913 -50.28331; 0.00000 0.00000 0.00000 1.00000; --------------------- Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; -0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable /Applications/freesurfer/7.2.0/average/mni305.cor.mgz Tmov: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.00857 0.02020 -0.00990 1.93629; -0.01789 1.03251 0.24795 -11.46406; 0.02556 -0.30660 1.20913 -50.28331; 0.00000 0.00000 0.00000 1.00000; Determinant 1.33659 subject = S0010_FS RegMat --------------------------- 1.00857 0.02020 -0.00990 1.93629; -0.01789 1.03251 0.24795 -11.46406; 0.02556 -0.30660 1.20913 -50.28331; 0.00000 0.00000 0.00000 1.00000; UnZeroing CRAS for fstal output xfm Any help would be greatly appreciated. Isabelle

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slice timing for multiband fMRI
by Laura Doll 04 Apr '22

04 Apr '22

External Email - Use Caution Hi everyone, We are currently piloting an fMRI measurement with multiband sequence on a 3T Siemens scanner to increase resolution, but I don't know how to do the slice timing correction: I assume, that I have to use a slicedelay file instead of the usual up/down/even/odd/siemens flags? But how do I know which slices were excited simultaneously? Our multiband acceleration factor is 2, if I got our MRI physicist correctly, GRAPPA acceleration is also 2, and we are using a TR of 2s. More details of the sequence are in the attached pdf (which is unfortunately in German). Looking forward to any suggestions. Best, Laura

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Questions regarding ROI creation for SPM based on FreeSurfer parcellation
by Falko Mecklenbrauck 04 Apr '22

04 Apr '22

External Email - Use Caution Dear FreeSurfer-Experts, I’m in need of your experience to help me with a decision in my current project: I want to use certain areas, that were identified by structural graph theoretical analyses based on the FreeSurfer parcellation and DTI data, as Regions of interest in SPM. We already have a script that helps with the transfer and creation of ROIs however it is still unclear what’s the best way to create the ROIs. Here are a few of my ideas and pros and cons regarding these: 1. Parcel the MNI T1 standard brain used in SPM with FreeSurfer and create the ROIs from the identified regions from that PRO: direct use of the standard space, that is later used in SPM’s group level analysis CON: SPM tends to be peculiar in giving information about their standard template, so I am unsure if the one I found in the spm12-folder is the correct one to use 2. Extract the ROIs of each participant individually and then use SPM to normalize and averaging/summing these PRO: Ending up in same space as the SPM analysis CON: identified regions are (at the moment) not individually identified, although they could be; normalization is difficult with just ROIs ALTERNATIVE: use FreeSurfer not on individual “raw” T1 images but on already normalized T1 images and then do the ROIs individually per participant. Probably, I am also forgetting another possibility. I am looking forward to hearing your ideas and comments. Thank you very much in advance, Best wishes, Falko

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Freesurfer March 2022