Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Mismatched dimensions with T1 and Flair inputs
by Vilde 08 Oct '14

08 Oct '14

Dear mailing list, I am trying to do a recon-all with two nifti inputs: A T1 and a Flair, for pial surface refinement. This results in an error message saying the dimensions are mismatched. (The third dimension of the T1 and Flair are different by one slice. ) I do not, however, have a problem running recon-all with only one T1 input. I am using Freesurfer v 5.1 . I read in the release notes that in version 5.2 you can use the flag -FLAIR when you are using a flair image as input. I suppose this will not run in an earlier version? Would it be correct to use the following command : recon-all -s [subject] -i T1.nii -i flair.nii -all Kind regards,Vilde

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Re: [Freesurfer] Surface Viewer Issue.
by Gregory Kirk 08 Oct '14

08 Oct '14

i saw this problem on one redhat installation, not on any others, seems something with the X library orientation information and openGL greg On 10/08/14, Jamie Hanson wrote: > Hi Freesurfer List, > > > I had a (hopefully quick) question about surface viewers and data orientation in tksurfer v. freeview. > > > I processed all my data in freesurfer v5.3.0 (on a linux cluster) and noticed something odd when I viewed surfaces. For tksurfer, the surfaces were upside down when I opened them (see attached pic: tksurfer.png); for freeview, the data looked fine (see attached pic: freeview.png). > > > I believe the orientation of the images is correct (judging by the freeview axes), but wondered if this was something others had run into? I uploaded an example subject to the Martinos Center FileDrop (link: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=9491zcnivqw) > > > Any thoughts are greatly appreciated! Thanks much! > > > Best, > Jamie. > > > > -- > Jamie L. Hanson > Postdoctoral Fellow, Carolina Consortium on Human Development > Duke University > 417 Chapel Drive > Duke West Campus > Sociology-Psychology Building, Room 07A > Durham, NC 27710 > Email: jamielarshanson(a)gmail.com > Website: http://jamiehanson.org/

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Surface Viewer Issue.
by Jamie Hanson 08 Oct '14

08 Oct '14

Hi Freesurfer List, I had a (hopefully quick) question about surface viewers and data orientation in tksurfer v. freeview. I processed all my data in freesurfer v5.3.0 (on a linux cluster) and noticed something odd when I viewed surfaces. For tksurfer, the surfaces were upside down when I opened them (see attached pic: tksurfer.png); for freeview, the data looked fine (see attached pic: freeview.png). I believe the orientation of the images is correct (judging by the freeview axes), but wondered if this was something others had run into? I uploaded an example subject to the Martinos Center FileDrop (link: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=9491zcnivqw) Any thoughts are greatly appreciated! Thanks much! Best, Jamie. -- Jamie L. Hanson Postdoctoral Fellow, Carolina Consortium on Human Development Duke University 417 Chapel Drive Duke West Campus Sociology-Psychology Building, Room 07A Durham, NC 27710 Email: jamielarshanson(a)gmail.com Website: http://jamiehanson.org/

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Running GCA atlas, problem with talairach
by N/A N/A 08 Oct '14

08 Oct '14

Hi Freesurfers, I am trying to make an atlas using the GCA algorithm and the error message I just got is asking for the talairach.xfm file. The scans I am using were originally run through freesurfer 3.1 and talairach processing was not done. What do you suggest I do to use these scans in my new atlas? Kind regards, Alexarae

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Re: [Freesurfer] sequence advice for GE 750 & 8-channel coil
by Antonio Algaze Beato 08 Oct '14

08 Oct '14

Hello Lee - thanks so much for your response. I looked into the document you referred me to and found a section on GE protocols here (page 3): http://martinos.org/~andre/FreeSurfer_recommended_morphometry_protocols.pdf I would appreciate your input on a few details. First, the document indicates "min (9150ms) for the TR value. However, the minimum TR is about 8 ms when I prescribe a similar IR-FSPGR sequence. I may be missing something obvious, but: a) Would that be 9.15 ms instead? (actually, the TR is not selectable when prescribing this 3D sequence). Also, we are mostly interested in getting good whole-brain segmentation and, from what I gather, the document mentions that multiecho FLASH is the way to go for this. b) Would the GE IR-FSPGR sequence specified in the protocol document still be OK for getting reliable whole-brain segmentation? c) I take it then that there is no "GE-version" for the multiecho FLASH, correct? Thanks again, Antonio

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cortical and subcortical masks in txt
by stdp82＠virgilio.it 08 Oct '14

08 Oct '14

Hi list, I need to extract the cortical and subcortical masks created by using recon-all as .txt. I would work on the txt to import FS masks in Brain Voyager Qx which does not accept .nii.gz but only .par/.rec format. Thanks Best regards, Stefano

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Comparison of surface and euclidean distances of fsaverage
by pfannmoelj＠uni-greifswald.de 08 Oct '14

08 Oct '14

Dear FreeSurfer experts, I computed distances on the cortex surface of fsaverage using mris_pmake. The exact syntax of the distance computation was: mris_pmake --subject fsaverage --hemi lh/rh --surface0 smoothwm --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:XXXXX,endVertex:XXXXX . Subsequently, the euclidean distance was computed using the MNI coordinates displayed by tksurfer if the startVertex and the stopVertex are selected: distance_euc = sqrt[(startMNI_x-stopMNI_x)^2+(startMNI_y-stopMNI_y)^2+(startMNI_z-stopMNI_z)^2] . The in-surface distance must be larger or equal to the euclidean distance. However, in ~50% of the cases investigated the opposite is computed. Typical distances calculated are in the range of 7 mm. Do you have an explanation for this outcome and a possible solution? How can it be corrected? I am using FreeSurfer 5.3 and did not encounter any other problems in data evaluation. Any help us highly appreciated! Sincerely yours pfannmoe

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Gyrification index vs cortical surface area
by Knut J Bjuland 07 Oct '14

07 Oct '14

Dear FreeSurfer experts I have run analyses on gyrification index. I was wondering if anybody could tell me what exactly is the relationship between gyrification index and cortical area. My gyrification results and area results are to a large extent similar. Am I measuring approximately the same thing? Thank you Knut Jørgen Bjuland PhD candidate The Norwegian University of Science and Technology (NTNU) Trondheim, Norway

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sequence advice for GE 750 & 8-channel coil
by Antonio Algaze Beato 06 Oct '14

06 Oct '14

Dear Freesurfer users, Greetings from Puerto Rico. I am new to FS and would appreciate it very much if you could share some suggestions on appropriate parameters for a GE 750 3T using an 8-channel coil and running system software v. 23.1. I searched the list for these, but could not find anything relatively recent. Your help will be greatly appreciated. Cheers, Antonio

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Visualizing individual ROI labels
by Elissa McIntosh 06 Oct '14

06 Oct '14

Hello freesurfer experts, I am hoping that someone can tell me how I can create 3D representations of individual cortical ROIs (labels based on the Desikan/Killiany Atlas) to be used in figures. I'm trying to make figures that show the ROIs that I investigated (like this figure in Desikan et al. paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012853) I know that I can manually make a label in qdec, but I was hoping that there was an automated method to highlighting individual labels/ROIs. Thank you, Elissa

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