Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

Eklund's 2016 and FreeSurfer
by Sahil Bajaj 27 Nov '17

27 Nov '17

Hi, I was wondering if there is any paper published by FreeSurfer team or FreeSurfer experts (after Eklund's 2016 paper) stating that the cluster failure issue is not an issue in FreeSurfer toolbox and/or whether CFT of less than 0.05 or 0.01 to estimate cortical thickness/volume/area maps is fine to use if Monte-Carlo simulations (MCZ) in FreeSurfer. I am looking for any such paper to cite in one of my papers I am working on. Thanks ! Sahil

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make_average_subject label files
by M del Mar Velasco 27 Nov '17

27 Nov '17

Dear Freesurfer experts, I have a question related to make_average_subject command and Freesurfer versions. When I used to create my average subject with Freesurfer 5.3, I got lh.cortex.label and rh.cortex.label files inside label folder with 149955 vertexs. Moreover, lh.Medial_Wall.label and rh.Medial_Wall.label had 13887 vertexs. However, with new Freesurfer 6, I get 163841 vertexs for cortex and only one vertex for medial wall. That's why I have problems with mri_glmfit when I use rh or lh.cortex.label files as label mask. I am considering all vertexs, and I would like to use only real cortex vertexs. Are label files outputs from make_average_subject wrong? How can I fit this problem? Thanks in advance, M del Mar

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Back to native space after registration
by Avideh Gharehgazlou 27 Nov '17

27 Nov '17

Hi experts, Will you please briefly explain to me the rationale behind why subjects put back into their original space after alignment to the template (fsaverage)? and also, how this is done. Thanks so much, Avi 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. AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout fichier qui y est joint, est reserve à l'usage exclusif du destinataire visé et peut contenir des renseignements confidentiels et privilégiés. Toute lecture, utilisation, divulgation ou distribution non autorisée est interdite. Si vous n'êtes pas le destinataire visé, veuillez en aviser l'expéditeur par retour de courriel et détruire toutes les copies du message original.

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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.

2 1

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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