Freesurfer November 2017

freesurfer@nmr.mgh.harvard.edu

110 participants
198 discussions

Re: [Freesurfer] hippocampal subfields stats
by Iglesias Gonzalez, Eugenio 27 Nov '17

27 Nov '17

Dear Donatas, I believe that mri_segstats is just counting voxels using the hard segmentation, whereas the volume in lh.hippoSfVolumes-T1.long.v20.txt is obtained using a soft segmentation. If you’re interested in this, look up the WRITE_POSTERIORS option in the wiki. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 21/11/2017, 18:00, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Donatas Sederevicius" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of donatas.sederevicius(a)psykologi.uio.no> wrote: Dear Freesurfer Developers, I’ve run the new longitudinal hippocampal subfields segmentation using Freesurfer’s developer version. Then I decided to extract stats for each hierarchy: HBT, FS60 and CA. I used the following command, for example: mri_segstats —seg lh.hippoAmygLabels-T1.long.v20.CA.mgz —ctab-default —sum output.txt I got what I wanted but decided to compare the results of one subject for Hippocampal_tail for each hierarchy and with the text file lh.hippoSfVolumes-T1.long.v20.txt. I got the following volume values: lh.hippoSfVolumes-T1.long.v20.txt: 583.65 HBT: 593.4 FS60: 593.4 CA: 598.3 I wonder how do you actually extract stats that are present in lh.hippoSfVolumes-T1.long.v20.txt file? What is the reason for different values? I’m very curious since I cannot get the exact same stats as in the lh.hippoSfVolumes-T1.long.v20.txt file. Thanks a lot! Donatas _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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LGI
by 郑凤莲 27 Nov '17

27 Nov '17

Hi experts, I am using Freesurfer 6.0 for LGI. I ran recon-all and got the map of LGI. My question is that can I get the specific value of every gyrus as the value of thickness in the file of lh.aparc.stats? I can't find it from stats direction. Thanks a lot ! Zheng

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Qdec
by 郑凤莲 27 Nov '17

27 Nov '17

Hi professors, I am using Qdec in Freesurfer. I want to study the relationships between age and cortical thickness, age and cortical volume, age and surface area. Is it necessary to corrected by eTIV for volume and surface area in Qdec? I am looking forward to your reply. Thanks, Zheng

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CSF mask with aparc+aseg
by Sam D 26 Nov '17

26 Nov '17

Hello, I am attempting to generate a CSF mask from my aparc+aseg.nii image file. However, my mask seems to only encompass the ventricular system itself, ignoring any other CSF (see attached image). I attempted to make the mask using the following MRI_binarize command with FS labels. mri_binarize --i aparc+aseg.nii --match 4, 5, 14, 15 24, 31, 43, 44, 63, 122, 221, 257 --o CSF_test.nii The labels corresponded to the structures listed below, including label 24, CSF. I assumed this would capture non-ventricular CSF. Has anyone else encountered this issue? Any help would be greatly appreciated! 4 Left-Lateral-Ventricle 120 18 134 0 5 Left-Inf-Lat-Vent 196 58 250 0 14 3rd-Ventricle 204 182 142 0 15 4th-Ventricle 42 204 164 0 24 CSF 60 60 60 0 31 Left-choroid-plexus 0 200 200 0 43 Right-Lateral-Ventricle 120 18 134 0 44 Right-Inf-Lat-Vent 196 58 250 0 63 Right-choroid-plexus 0 200 221 0 122 CSF-SA 74 255 74 0 221 Inf_Lat_Vent 197 58 250 0 257 CSF-ExtraCerebral 60 60 60 0 *Sam DeWitt, Ph.D.Postdoctoral FellowPediatric Mood and Anxiety Disorders ProgramDepartment of PsychiatryIcahn School of Medicine at Mount Sinai1240 Park Avenue, New York, NY 10029Tel: (212)241-0893 <(212)%20241-0893>*

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Local white and gray matter measures
by Crocetti, Deana 26 Nov '17

26 Nov '17

Freesurfer Developers, I recently received FS data from a collaborator which included measures such for which, I as a FS user, I am familiar (i.e. GrayVol.lh.Frontal and GrayVol.rh.Frontal). Also included were the following 2 variables: Local_Gray_Matter and Local_White_Matter. I have not come across these measures in my use of FS. My questions are: 1) are these variables part of FS output? If so, what output file contains them? 2) if they are FS variables, what do these measures (Local_Gray_Matter and Local_White_Matter) include? Thank you in advance for your time, Deana ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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data conversion
by Danny Deng 26 Nov '17

26 Nov '17

Dear FS devleopers, I tried to utilize tutorial data-set to practice data conversion but encountered problems as follow: I located the data by SUBJECT_DIR and tried first step but failed as attached pic displayed. Hope you can help. Thanks. Best Regards, Danny Deng

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inqiury
by Danny Deng 26 Nov '17

26 Nov '17

Dear FS developers, I wish to transform DICOM format to omgz format. However, we have problem when we tried to do recon-all command. The error is as follow: bash-3.2$ export FREESURFER_HOME=/applications/freesurfer bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni bash-3.2$ sudo recon-all -s 'aaa' -i /Users/Dannydeng/desktop/danny_mri/MR22022/DICOM/IM_0001 Password: FREESURFER_HOME: Undefined variable. bash-3.2$ Thanks. Best Regards, Danny Deng

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Talairach of ROI and FindClustersAndGotoMax
by Dongsheng Wu 25 Nov '17

25 Nov '17

Dear Freesurfer Developers, I have two questions about coordinate of ROI when running the QDEC module: (1) After drawing a ROI,the terminal demostrated the results like this: ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 -4.407 13586 966.10 44.2 -39.2 7.1 0.02020 0.01840 0.02200 2402 -4786.73 bankssts Could you tell me what exactly the "TalX TalY TalZ" refers to and whether the coordinate "TalX TalY TalZ" represents the VtxMax of the ROI? When I clicked the button "FindClustersAndGotoMax", the terminal showed the results: ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 -1.6946 7 966.10 45.9 -43.8 7.5 2402 bankssts The size(966.10mm2) and NVtxs(2402) of the two results are the same, but the "Tal X Y Z" is a little different. So are they the same region? (2) I used mris_anatomical_stats to get a set of statistics on each individual label created before, the average thickness,number of vertices, surface area and gray matter volume were saved in the file of stat. Was the average thickness the normalized one? Thank you for your help. Best regards, Dongsheng Wu Huaxi MR Research Center, Westchina Hospital,Sichuan University Chengdu,Sichuan,China

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Create mpm label files
by Luqi Cheng 25 Nov '17

25 Nov '17

Dear freesurfer experts, I have several individual surface label files (eg, lh.MT.label)in the same region, how could I merge them and create a max probability map surface label file? Thank you very much. Best, Luqi

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Re: [Freesurfer] mri_gtmpvc error: failed tissue type check
by Douglas Greve 25 Nov '17

25 Nov '17

sorry, can you send me the details again? On 11/21/17 10:24 AM, Klein, Gregory wrote: > Hello Donatas and Douglas, > > Did you ever find a cause and solution for this problem? I too > occasionally get this error message, and cannot get the results of > mri_gtmpvc for certain subjects. > > Any suggestions are welcome. > Thanks, > Greg > > -- > Gregory Klein, PhD > Principal Scientist, Biomarker Experimental Medicine Leader > F. Hoffmann-La Roche Ltd. > Bldg 01, Floor 16, N445 > Grenazacherstrasse 170, > 4070 Basel, Switzerland > Mobile: +41 79 572 97 89 > Office Phone: +41 61 682 07 59 > email: gregory.klein(a)roche.com <mailto:gregory.klein@roche.com> > > Roche Products Limited, 6 Falcon Way, Shire Park, Welwyn Garden City, > AL7 1TW Registration No:100674 > > Confidentiality note: This message is intended for the use of the > named recipient(s) only and may contain confidential and / or > privileged information. If you are not the intended recipient, please > contact the sender and delete this message. Any unauthorized use of > the information contained in this message is prohibited.

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Freesurfer November 2017