Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats
Thanks Doug, I used the first link and works perfectly now! Best regards, Amirhossein Manzouri On Tue, May 20, 2014 at 5:03 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: I just ran it, and it works fine. It may be that I need to give you more libraries. Start with this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsutils.py Copy it into $FREESURFER_HOME/bin (after making a backup of the original one) If that still does not work, then copy this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsutils.pyc doug On 05/20/2014 04:36 AM, amirhossein manzouri wrote: Dear Doug, Kindly find attached a sample of my lh.aparc.stats file! Best regards, Amirhossein Manzouri On Mon, May 19, 2014 at 7:59 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Can you send me your lh.aparc.stats file? doug On 05/14/2014 01:41 PM, amirhossein manzouri wrote: Yes! On May 14, 2014 7:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Is the mean thickness in the ?h.aparc.stats file? Something like # Measure Cortex, MeanThickness, Mean Thickness, 2.27227, mm On 05/13/2014 05:18 PM, amirhossein manzouri wrote: Hi, The same result! the last is insula ! Best regards, Amirhossein Manzouri On Mon, May 12, 2014 at 5:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ greve/aparcstats2table On 05/12/2014 03:41 AM, amirhossein manzouri wrote: Hi again, I think I missed my question, How can I get the Mean Thickness of each hemisphere for several subjects using the aparcstats2table command? On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com wrote: Dear Doug, I have read this post( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25218.html ) regarding extracting Mean Cth of each hemisphere and I just get insula as the last and totally 34 numbers, I use aparcstats2table --hemi lh --subjects bert -m thickness --tablefile lh.Cth.bert.txt Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
[Freesurfer] Fwd: Welcome to the Freesurfer mailing list
im get it -- Forwarded message -- From: freesurfer-requ...@nmr.mgh.harvard.edu Date: Wed, 21 May 2014 09:51:02 -0400 Subject: Welcome to the Freesurfer mailing list To: bara9...@gmail.com Welcome to the Freesurfer@nmr.mgh.harvard.edu mailing list! To post to this list, send your email to: freesurfer@nmr.mgh.harvard.edu General information about the mailing list is at: https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer If you ever want to unsubscribe or change your options (eg, switch to or from digest mode, change your password, etc.), visit your subscription page at: https://mail.nmr.mgh.harvard.edu/mailman/options/freesurfer/bara9114%40gmail.com You can also make such adjustments via email by sending a message to: freesurfer-requ...@nmr.mgh.harvard.edu with the word `help' in the subject or body (don't include the quotes), and you will get back a message with instructions. You must know your password to change your options (including changing the password, itself) or to unsubscribe. It is: BaRa9114 Normally, Mailman will remind you of your nmr.mgh.harvard.edu mailing list passwords once every month, although you can disable this if you prefer. This reminder will also include instructions on how to unsubscribe or change your account options. There is also a button on your options page that will email your current password to you. 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Desikan Killiany Atlas measurements
Dear all, I want to get the measurements of meancurvature, thickness, white matter volume and gray matter volume based on Desikan-Killiay Atlas. I would like to learn whether the commands I used to get them are the correct ones (in terms of content) for Desikan Killiany atlas? *For meancurv: * aparcstats2table --hemi lh --subjects S1 S2 S3 --parc aparc --meas meancurv -t lh.parc.meancurv.txt *For thickness:* aparcstats2table --hemi rh --subjects S1 S2 S3 --parc aparc --meas meancurv -t rh.parc.meancurv.txt *For WM volume:* asegstats2table --all-segs --subjects S1 S2 S3 \-t table.wmparc.txt -d space --stats wmparc.stats *For GM volume:* aparcstats2table --subjects S1 S2 S3 --hemi lh --meas volume --parc=aparc --tablefile aparc_lh_volume_table.txt Thanks in advance, ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] CTABreadASCII error with mris_label2annot
Freesurfer folks, I'm trying to compile an annotation using mris_label2annot after transferring fsaverage5 labels to a single subject. I'm getting a strange error. Essentially it looks like it can't find most of my transferred labels, which doesn't make sense as they are definitely in the directory in which I'm executing the command. The same error happens with both hemispheres. I am including an 'unknown' entry in the ctab files. I've tried changing things around with my ctab files and it looks like it just won't take in anything past the first '-l' flag in the mris_label2annot command. *Reading ctab rh.Yeo_7Net_split.ctab* *Number of ctab entries 2* *$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $* *cwd /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/label* *cmdline mris_label2annot --s HS_001 --h rh --ctab rh.Yeo_7Net_split.ctab --annot Yeo_7Net_split_aparc --l rh.Background+FreeSurfer_Defined_Medial_Wall.label --l rh.7Networks_RH_Vis.label --l rh.7Networks_RH_SomMot.label --l rh.7Networks_RH_DorsAttn_Post.label --l rh.7Networks_RH_DorsAttn_FEF.label --l rh.7Networks_RH_DorsAttn_PrCv.label --l rh.7Networks_RH_SalVentAttn_TempOccPar.label --l rh.7Networks_RH_SalVentAttn_PrC.label --l rh.7Networks_RH_SalVentAttn_FrOper.label --l rh.7Networks_RH_SalVentAttn_PFCv.label --l rh.7Networks_RH_SalVentAttn_PFCl.label --l rh.7Networks_RH_SalVentAttn_Med.label --l rh.7Networks_RH_Limbic_OFC.label --l rh.7Networks_RH_Limbic_TempPole.label --l rh.7Networks_RH_Cont_Par.label --l rh.7Networks_RH_Cont_Temp.label --l rh.7Networks_RH_Cont_PFCv.label --l rh.7Networks_RH_Cont_PFCl.label --l rh.7Networks_RH_Cont_pCun.label --l rh.7Networks_RH_Cont_Cing.label --l rh.7Networks_RH_Cont_PFCmp.label --l rh.7Networks_RH_Default_Par.label --l rh.7Networks_RH_Default_Temp.label --l rh.7Networks_RH_Default_PFCv.label --l rh.7Networks_RH_Default_PFCm.label --l rh.7Networks_RH_Default_PCC.label * *sysname Linux* *hostname gauss.rad.msu.edu http://gauss.rad.msu.edu* *machine x86_64* *user beachpau* *subject HS_001* *hemirh* *SUBJECTS_DIR /extern/research/PI/training/beachpau/Beach_FreeSurfer_data* *ColorTable rh.Yeo_7Net_split.ctab* *AnnotName Yeo_7Net_split_aparc* *nlables 26* *LabelThresh 0 0.00* *Loading /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/surf/rh.orig* * 1 65793 rh.Background+FreeSurfer_Defined_Medial_Wall* * 2 -1 NOT_FOUND* * 3 -1 NOT_FOUND* * 4 -1 NOT_FOUND* * 5 -1 NOT_FOUND* * 6 -1 NOT_FOUND* * 7 -1 NOT_FOUND* * 8 -1 NOT_FOUND* * 9 -1 NOT_FOUND* *10 -1 NOT_FOUND* *11 -1 NOT_FOUND* *12 -1 NOT_FOUND* *13 -1 NOT_FOUND* *14 -1 NOT_FOUND* *15 -1 NOT_FOUND* *16 -1 NOT_FOUND* *17 -1 NOT_FOUND* *18 -1 NOT_FOUND* *19 -1 NOT_FOUND* *20 -1 NOT_FOUND* *21 -1 NOT_FOUND* *22 -1 NOT_FOUND* *23 -1 NOT_FOUND* *24 -1 NOT_FOUND* *25 -1 NOT_FOUND* *26 -1 NOT_FOUND* *Mapping unhit to unknown* *Found 5 unhit vertices* *Writing annot to /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/label/rh.Yeo_7Net_split_aparc.annot* I have attached my .ctab files in case they would help. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) lh.Yeo_7Net_split.ctab Description: Binary data rh.Yeo_7Net_split.ctab Description: Binary data ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] change background color in tksurfer
Hi Rujing, If you load the surface up in freeview you can change the background color. -Louis On Wed, 14 May 2014, charujing123 wrote: Hi Bruce and Doug, Ok, I see. That's all right. All the best. Rujing Zha 2014-05-14 charujing123 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2014-05-14 20:22 主题：Re: [Freesurfer] change background color in tksurfer 收件人：Freesurfer support listfreesurfer@nmr.mgh.harvard.edu 抄送： Sorry Rujing, I don't think we ever implemented that (although we should) On Wed, 14 May 2014, charujing123 wrote: Hi FS experts and users I want to change the background color of tksurfer from black to white. However I cannot find the drop-down list. Is there anyone who can tell me to desolve this? Thanks. All the best. Rujing Zha 2014-05-14 charujing123 ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal
Hi Anastasia, I have a large set of freesurfer recons (T1) already processed through FS version 5.2 longitudinal stream while ago. However, I see now that there is an advantage of using Tracula 5.3 longitudinal stream for DTI longitudinal analysis. Do you know if I run the DWI data using 5.3 TRACULA longitudinal stream - if it will work with recons that are processed with 5.2? Thanks! Y ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] R: R: R: R: R: R: Filipping issue
On 05/21/2014 08:30 AM, Paola Valsasina wrote: Dear Doug, thank you so much for your help, it worked! now I pre-processed the flipped images and estimated my GLM model. I had a look at my results with tksurfer, as explained in the xhemi tool page (e.g., tksurfer fsaverage_sym lh inflated -aparc -overlay my results/sig.mgh) I have now two (probably trivial) questions: 1) the default threshold of the overlay is the same as in qdec? And how can I change this threshold for visualization purposes? I'm not sure if the default is the same, I think it is. To change the threshold, Configure-Overlay 2) how can I obtain a list of clusters surviving to the threshold (i.e., the analogous of the Find Clusters and Go to Max button in Qdec)? Run mri_glmfit-sim. At this point it is the same as any other group analysis. See the tutorial and lecture notes doug Thank you in advance Kind regards Paola Paola Valsasina, MSc Research Fellow Neuroimaging Research Unit (Director Prof. M. Filippi) Institute of Experimental Neurology, Division of Neuroscience, Scientific Institute and University Vita-Salute San Raffaele Via Olgettina 60, 20132 Milan, Italy -- IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO PERCHE' QUI LA RICERCA DIVENTA CURA. CF 07636600962 SE NON QUI, DOVE? Info: 5xmi...@hsr.it - http://www.5xmille.org/ Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.com -Messaggio originale- Da: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Inviato: lunedì 19 maggio 2014 19.56 A: Valsasina Paola; Freesurfer@nmr.mgh.harvard.edu Oggetto: Re: R: R: R: R: R: [Freesurfer] Filipping issue Instead of --surfreg try using --srcsurfreg doug On 05/14/2014 04:37 AM, Paola Valsasina wrote: Dear Doug, thank you for your answer. I added --target fsaverage_sym but it still fails: MRISread($SUBJECTS_DIR/fsaverage_sym/surf/lh.fsaverage_sym.sphere.reg): could not open file. This seems to happen because in the folder fsaverage_sym/surf there is no lh.fsaverage_sym.sphere.reg; in this folder there is a file called lh.sphere.reg or a file called lh.ni.sym.b40.i30.sphere.reg. Which one is the correct file? Thank you again Best regards, Paola Paola Valsasina, MSc Research Fellow Neuroimaging Research Unit (Director Prof. M. Filippi) Institute of Experimental Neurology, Division of Neuroscience, Scientific Institute and University Vita-Salute San Raffaele Via Olgettina 60, 20132 Milan, Italy -- IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO PERCHE' QUI LA RICERCA DIVENTA CURA. CF 07636600962 SE NON QUI, DOVE? Info: 5xmi...@hsr.it - http://www.5xmille.org/ Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.com -Messaggio originale- Da: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Inviato: martedì 13 maggio 2014 21.12 A: Valsasina Paola; Freesurfer@nmr.mgh.harvard.edu Oggetto: Re: R: R: R: R: [Freesurfer] Filipping issue Sorry, in both of those mris_preproc commands add --target fsaverage_sym doug On 05/13/2014 09:48 AM, Paola Valsasina wrote: Dear Doug, I am trying to run mris_preproc as you indicated, but it fails with the following error: MRISread($SUBJECTS_DIR/fsaverage/surf/lh.fsaverage_sym.sphere.reg): could not open file. Why is target file searched in the fsaverage folder? I was expecting it is searched in the fsaverage_sym folder? Thank you in advance Kind regards Paola Paola Valsasina, MSc Research Fellow Neuroimaging Research Unit (Director Prof. M. Filippi) Institute of Experimental Neurology, Division of Neuroscience, Scientific Institute and University Vita-Salute San Raffaele Via Olgettina 60, 20132 Milan, Italy -- IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO PERCHE' QUI LA RICERCA DIVENTA CURA. CF 07636600962 SE NON QUI, DOVE? Info: 5xmi...@hsr.it - http://www.5xmille.org/ Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.com -Messaggio originale- Da: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Inviato: martedì 29 aprile 2014 18.25 A: Valsasina Paola; Freesurfer@nmr.mgh.harvard.edu Oggetto: Re: R: R: R: [Freesurfer] Filipping issue You can't use qdec for this, you will have to use mris_preproc, mri_surf2surf, mri_glmfit, and mri_glmfit-sim. The first step is the tricky one in that you will have to run mris_preproc twice then merge the two data sets. For the subjects that you want the left hemisphere, run mris_preproc as normal mris_preproc --hemi lh --meas thickness --surfreg fsaverage_sym.sphere.reg --s subject1 --s subject2 --o subjects.lh.sm00.mgh For the right hemi subjects run mris_preproc --hemi lh --meas thickness --surfreg fsaverage_sym.sphere.reg --s
Re: [Freesurfer] CTABreadASCII error with mris_label2annot
Your color table appears to have been created in windows (or maybe mac). Convert it to a unix text file. doug On 05/21/2014 10:40 AM, Paul Beach wrote: Freesurfer folks, I'm trying to compile an annotation using mris_label2annot after transferring fsaverage5 labels to a single subject. I'm getting a strange error. Essentially it looks like it can't find most of my transferred labels, which doesn't make sense as they are definitely in the directory in which I'm executing the command. The same error happens with both hemispheres. I am including an 'unknown' entry in the ctab files. I've tried changing things around with my ctab files and it looks like it just won't take in anything past the first '-l' flag in the mris_label2annot command. /Reading ctab rh.Yeo_7Net_split.ctab/ /Number of ctab entries 2/ / / /$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $/ /cwd /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/label/ /cmdline mris_label2annot --s HS_001 --h rh --ctab rh.Yeo_7Net_split.ctab --annot Yeo_7Net_split_aparc --l rh.Background+FreeSurfer_Defined_Medial_Wall.label --l rh.7Networks_RH_Vis.label --l rh.7Networks_RH_SomMot.label --l rh.7Networks_RH_DorsAttn_Post.label --l rh.7Networks_RH_DorsAttn_FEF.label --l rh.7Networks_RH_DorsAttn_PrCv.label --l rh.7Networks_RH_SalVentAttn_TempOccPar.label --l rh.7Networks_RH_SalVentAttn_PrC.label --l rh.7Networks_RH_SalVentAttn_FrOper.label --l rh.7Networks_RH_SalVentAttn_PFCv.label --l rh.7Networks_RH_SalVentAttn_PFCl.label --l rh.7Networks_RH_SalVentAttn_Med.label --l rh.7Networks_RH_Limbic_OFC.label --l rh.7Networks_RH_Limbic_TempPole.label --l rh.7Networks_RH_Cont_Par.label --l rh.7Networks_RH_Cont_Temp.label --l rh.7Networks_RH_Cont_PFCv.label --l rh.7Networks_RH_Cont_PFCl.label --l rh.7Networks_RH_Cont_pCun.label --l rh.7Networks_RH_Cont_Cing.label --l rh.7Networks_RH_Cont_PFCmp.label --l rh.7Networks_RH_Default_Par.label --l rh.7Networks_RH_Default_Temp.label --l rh.7Networks_RH_Default_PFCv.label --l rh.7Networks_RH_Default_PFCm.label --l rh.7Networks_RH_Default_PCC.label / /sysname Linux/ /hostname gauss.rad.msu.edu http://gauss.rad.msu.edu/ /machine x86_64/ /user beachpau/ / / /subject HS_001/ /hemirh/ /SUBJECTS_DIR /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/ /ColorTable rh.Yeo_7Net_split.ctab/ /AnnotName Yeo_7Net_split_aparc/ /nlables 26/ /LabelThresh 0 0.00/ /Loading /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/surf/rh.orig/ / 1 65793 rh.Background+FreeSurfer_Defined_Medial_Wall/ / 2 -1 NOT_FOUND/ / 3 -1 NOT_FOUND/ / 4 -1 NOT_FOUND/ / 5 -1 NOT_FOUND/ / 6 -1 NOT_FOUND/ / 7 -1 NOT_FOUND/ / 8 -1 NOT_FOUND/ / 9 -1 NOT_FOUND/ /10 -1 NOT_FOUND/ /11 -1 NOT_FOUND/ /12 -1 NOT_FOUND/ /13 -1 NOT_FOUND/ /14 -1 NOT_FOUND/ /15 -1 NOT_FOUND/ /16 -1 NOT_FOUND/ /17 -1 NOT_FOUND/ /18 -1 NOT_FOUND/ /19 -1 NOT_FOUND/ /20 -1 NOT_FOUND/ /21 -1 NOT_FOUND/ /22 -1 NOT_FOUND/ /23 -1 NOT_FOUND/ /24 -1 NOT_FOUND/ /25 -1 NOT_FOUND/ /26 -1 NOT_FOUND/ /Mapping unhit to unknown/ /Found 5 unhit vertices/ /Writing annot to /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/label/rh.Yeo_7Net_split_aparc.annot/ I have attached my .ctab files in case they would help. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] CTABreadASCII error with mris_label2annot
Oy. Thanks - that worked. On Wed, May 21, 2014 at 11:21 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Your color table appears to have been created in windows (or maybe mac). Convert it to a unix text file. doug On 05/21/2014 10:40 AM, Paul Beach wrote: Freesurfer folks, I'm trying to compile an annotation using mris_label2annot after transferring fsaverage5 labels to a single subject. I'm getting a strange error. Essentially it looks like it can't find most of my transferred labels, which doesn't make sense as they are definitely in the directory in which I'm executing the command. The same error happens with both hemispheres. I am including an 'unknown' entry in the ctab files. I've tried changing things around with my ctab files and it looks like it just won't take in anything past the first '-l' flag in the mris_label2annot command. /Reading ctab rh.Yeo_7Net_split.ctab/ /Number of ctab entries 2/ / / /$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $/ /cwd /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/label/ /cmdline mris_label2annot --s HS_001 --h rh --ctab rh.Yeo_7Net_split.ctab --annot Yeo_7Net_split_aparc --l rh.Background+FreeSurfer_Defined_Medial_Wall.label --l rh.7Networks_RH_Vis.label --l rh.7Networks_RH_SomMot.label --l rh.7Networks_RH_DorsAttn_Post.label --l rh.7Networks_RH_DorsAttn_FEF.label --l rh.7Networks_RH_DorsAttn_PrCv.label --l rh.7Networks_RH_SalVentAttn_TempOccPar.label --l rh.7Networks_RH_SalVentAttn_PrC.label --l rh.7Networks_RH_SalVentAttn_FrOper.label --l rh.7Networks_RH_SalVentAttn_PFCv.label --l rh.7Networks_RH_SalVentAttn_PFCl.label --l rh.7Networks_RH_SalVentAttn_Med.label --l rh.7Networks_RH_Limbic_OFC.label --l rh.7Networks_RH_Limbic_TempPole.label --l rh.7Networks_RH_Cont_Par.label --l rh.7Networks_RH_Cont_Temp.label --l rh.7Networks_RH_Cont_PFCv.label --l rh.7Networks_RH_Cont_PFCl.label --l rh.7Networks_RH_Cont_pCun.label --l rh.7Networks_RH_Cont_Cing.label --l rh.7Networks_RH_Cont_PFCmp.label --l rh.7Networks_RH_Default_Par.label --l rh.7Networks_RH_Default_Temp.label --l rh.7Networks_RH_Default_PFCv.label --l rh.7Networks_RH_Default_PFCm.label --l rh.7Networks_RH_Default_PCC.label / /sysname Linux/ /hostname gauss.rad.msu.edu http://gauss.rad.msu.edu/ /machine x86_64/ /user beachpau/ / / /subject HS_001/ /hemirh/ /SUBJECTS_DIR /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/ /ColorTable rh.Yeo_7Net_split.ctab/ /AnnotName Yeo_7Net_split_aparc/ /nlables 26/ /LabelThresh 0 0.00/ /Loading /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/surf/rh.orig/ / 1 65793 rh.Background+FreeSurfer_Defined_Medial_Wall/ / 2 -1 NOT_FOUND/ / 3 -1 NOT_FOUND/ / 4 -1 NOT_FOUND/ / 5 -1 NOT_FOUND/ / 6 -1 NOT_FOUND/ / 7 -1 NOT_FOUND/ / 8 -1 NOT_FOUND/ / 9 -1 NOT_FOUND/ /10 -1 NOT_FOUND/ /11 -1 NOT_FOUND/ /12 -1 NOT_FOUND/ /13 -1 NOT_FOUND/ /14 -1 NOT_FOUND/ /15 -1 NOT_FOUND/ /16 -1 NOT_FOUND/ /17 -1 NOT_FOUND/ /18 -1 NOT_FOUND/ /19 -1 NOT_FOUND/ /20 -1 NOT_FOUND/ /21 -1 NOT_FOUND/ /22 -1 NOT_FOUND/ /23 -1 NOT_FOUND/ /24 -1 NOT_FOUND/ /25 -1 NOT_FOUND/ /26 -1 NOT_FOUND/ /Mapping unhit to unknown/ /Found 5 unhit vertices/ /Writing annot to /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/label/rh.Yeo_7Net_split_aparc.annot/ I have attached my .ctab files in case they would help. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine -
Re: [Freesurfer] Desikan Killiany Atlas measurements
Thank you so much! Can I also learn what is the difference between the gray matter values in lh.aparc.stats file and the gray matter values from the command below; aparcstats2table --subjects S1 S2 S3 --hemi lh --meas volume--parc=aparc --tablefile aparc_lh_volume_table.txt Thanks, -- 21 May 2014 tarihinde 18:19 saatinde, Douglas N Greve gr...@nmr.mgh.harvard.edu şunları yazdı: mostly right, a few corrections below On 05/21/2014 10:35 AM, Buse Merve Ürgen wrote: Dear all, I want to get the measurements of meancurvature, thickness, white matter volume and gray matter volume based on Desikan-Killiay Atlas. I would like to learn whether the commands I used to get them are the correct ones (in terms of content) for Desikan Killiany atlas? *For meancurv: * aparcstats2table --hemi lh --subjects S1 S2 S3 --parc aparc --meas meancurv -t lh.parc.meancurv.txt --parc=aparc *For thickness:* aparcstats2table --hemi rh --subjects S1 S2 S3 --parc aparc --meas meancurv -t rh.parc.meancurv.txt Use--parc=aparc --meas thickness -t rh.parc.thickness.txt *For WM volume:* asegstats2table --all-segs --subjects S1 S2 S3 \-t table.wmparc.txt -d space --stats wmparc.stats *For GM volume:* aparcstats2table --subjects S1 S2 S3 --hemi lh --meas volume--parc=aparc --tablefile aparc_lh_volume_table.txt Thanks in advance, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Desikan Killiany Atlas measurements
aparc.stats has all of the values (eg, thickness, area, volume, curv) for each ROI for a single subject. When you run aparcstats2table, you extract one of those for each subject for all ROIs and put them into a single table file On 05/21/2014 01:21 PM, Buse Merve Urgen wrote: Thank you so much! Can I also learn what is the difference between the gray matter values in lh.aparc.stats file and the gray matter values from the command below; aparcstats2table --subjects S1 S2 S3 --hemi lh --meas volume--parc=aparc --tablefile aparc_lh_volume_table.txt Thanks, -- 21 May 2014 tarihinde 18:19 saatinde, Douglas N Greve gr...@nmr.mgh.harvard.edu şunları yazdı: mostly right, a few corrections below On 05/21/2014 10:35 AM, Buse Merve Ürgen wrote: Dear all, I want to get the measurements of meancurvature, thickness, white matter volume and gray matter volume based on Desikan-Killiay Atlas. I would like to learn whether the commands I used to get them are the correct ones (in terms of content) for Desikan Killiany atlas? *For meancurv: * aparcstats2table --hemi lh --subjects S1 S2 S3 --parc aparc --meas meancurv -t lh.parc.meancurv.txt --parc=aparc *For thickness:* aparcstats2table --hemi rh --subjects S1 S2 S3 --parc aparc --meas meancurv -t rh.parc.meancurv.txt Use--parc=aparc --meas thickness -t rh.parc.thickness.txt *For WM volume:* asegstats2table --all-segs --subjects S1 S2 S3 \-t table.wmparc.txt -d space --stats wmparc.stats *For GM volume:* aparcstats2table --subjects S1 S2 S3 --hemi lh --meas volume--parc=aparc --tablefile aparc_lh_volume_table.txt Thanks in advance, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] kvlQuantify naming problem [possible fix]
Hello all, My site has recently upgraded to the newest version of Freesurfer, and I've run a set of subjects on recon-all using the hippocampal subfield segmentation flag. Everything went well. Then in running kvlQuantifyHippocampalSubfieldSegmentations.sh, I received error messages indicating that certain expected files didn't exist. In particular, among output files labeled with the scheme $subj/mri/posterior_$side_$struct.mgz, the script expected ...CA2-3.mgz and ...CA4-DG.mgz, and existing files were named ...CA2_3.mgz and ...CA4_DG.mgz -- in other words, the script expected a hyphen but instead the filenames contained an underscroe. After renaming the files appropriately, kvlQuantify... successfully generated the nonPartialVolumeStats files and everything worked fine. I didn't see any threads with this solution, and only one or two that mentioned the problem (http://bit.ly/1vHbV5K), so I thought I'd offer it up in case it could be addressed in a future release. Cheers, C.P. Frost ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] recon-all mri_nu_correct error
Hi Freesurfer experts, I was running recon-all on a cluster and encountered the following error: mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux compute-g20-12.deepthought.umd.edu 2.6.18-371.3.1.el5 #1 SMP Mon Nov 11 03:23:58 EST 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s hcp80100307 exited with ERRORS at Wed May 21 12:43:36 EDT 2014 Any idea whats the source of the error? Thanks! On Wed, May 21, 2014 at 2:20 PM, C.P. Frost cpfr...@wisc.edu wrote: Hello all, My site has recently upgraded to the newest version of Freesurfer, and I've run a set of subjects on recon-all using the hippocampal subfield segmentation flag. Everything went well. Then in running kvlQuantifyHippocampalSubfieldSegmentations.sh, I received error messages indicating that certain expected files didn't exist. In particular, among output files labeled with the scheme $subj/mri/posterior_$side_$struct.mgz, the script expected ...CA2-3.mgz and ...CA4-DG.mgz, and existing files were named ...CA2_3.mgz and ...CA4_DG.mgz -- in other words, the script expected a hyphen but instead the filenames contained an underscroe. After renaming the files appropriately, kvlQuantify... successfully generated the nonPartialVolumeStats files and everything worked fine. I didn't see any threads with this solution, and only one or two that mentioned the problem (http://bit.ly/1vHbV5K), so I thought I'd offer it up in case it could be addressed in a future release. Cheers, C.P. Frost ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] mri_convert frame error in tracula
Dear All, As suggested, I am reposting a previous question. I am trying to run a single subject in TRACULA (trac-all -corr -c config), 148, for who there is a folder ‘1482’ with all DWI DICOMs and a folder ‘ESNA148’ with the recon-all processing (Freesurfer 5.3). Also in $SUBJECTS_DIR there is bval.bval and bvec.bvec. I attached the trac-all.log that comes with the following error: ERROR: fMRIframe: frame = frames Can anyone help me? Thank you in advance! Regards, Pedro Rosa. trac-all.log Description: Binary data ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] kvlQuantify naming problem [possible fix]
Follow-up: I then run into indexing problems when calling freeview with subfield volumes (similar to http://bit.ly/1pdEWRZ), which leads me to believe kvlQuantify is the only script that relies on the old convention. Changing the names back to CA2_3.mgz, etc., fixes THAT problem. Rather than changing the filenames to the old convention, it's probably better to fix the script and leave the filenames alone. On Wed, May 21, 2014 at 1:06 PM, C.P. Frost car...@gmail.com wrote: Hello all, My site has recently upgraded to the newest version of Freesurfer, and I've run a set of subjects on recon-all using the hippocampal subfield segmentation flag. Everything went well. Then in running kvlQuantifyHippocampalSubfieldSegmentations.sh, I received error messages indicating that certain expected files didn't exist. In particular, among output files labeled with the scheme $subj/mri/posterior_$side_$struct.mgz, the script expected ...CA2-3.mgz and ...CA4-DG.mgz, and existing files were named ...CA2_3.mgz and ...CA4_DG.mgz -- in other words, the script expected a hyphen but instead the filenames contained an underscroe. After renaming the files appropriately, kvlQuantify... successfully generated the nonPartialVolumeStats files and everything worked fine. I didn't see any threads with this solution, and only one or two that mentioned the problem (http://bit.ly/1vHbV5K), so I thought I'd offer it up in case it could be addressed in a future release. Cheers, C.P. Frost ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] surface-based morphometry registration
Hi all, If I understand correctly, the surface-based morphometry (SBM) done by Freesurfer offers superior registration as compared to voxel-based methods such as VBM, in that: 1. SBM smoothing respects anatomical boundaries better than the 3D VBM smoothing. 2. SBM group analysis employs inter-subject alignment based on the patterns of sulci and gyri, as opposed to Talairach registration, which often ignores sulcal/gyral landmarks I'm not sure I understand those reasons, however. For 1., why does the smoothing operation (basically, a multiplication) care about anatomy or registration at all, such that it can be said it is better done in SBM vs VBM? And for 2., doesn't the Talairach registration used in VBM simply imply a certain target template? Surely such a template is used in SBM registration as well, and if that is the case, then how are sulcal/gyral landmarks taken into account? Thanks for any help! Tudor ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] surface-based morphometry registration
Hi Tudor 1. The smoothing we do is along the surface, so no matter how huge the kernel gets it only ever includes cortical gray matter. In contrast, volume smoothing kernels will happily smooth in white matter, skull, csf, the bore of the scanner, etc as the kernels get big. 2. Yes, we have a template, but it is a geometric one and not simply an average, so part of the advantage is higher dimensional nonlinear warping (which also exists in the volume), but part is that we register based on cortical folding patterns not image intensities, so folds are much more likely to align across subjects (and architectonic areas as well) cheers Bruce On Wed, 21 May 2014, Tudor Popescu wrote: Hi all, If I understand correctly, the surface-based morphometry (SBM) done by Freesurfer offers superior registration as compared to voxel-based methods such as VBM, in that: 1. SBM smoothing respects anatomical boundaries better than the 3D VBM smoothing. 2. SBM group analysis employs inter-subject alignment based on the patterns of sulci and gyri, as opposed to Talairach registration, which often ignores sulcal/gyral landmarks I'm not sure I understand those reasons, however. For 1., why does the smoothing operation (basically, a multiplication) care about anatomy or registration at all, such that it can be said it is better done in SBM vs VBM? And for 2., doesn't the Talairach registration used in VBM simply imply a certain target template? Surely such a template is used in SBM registration as well, and if that is the case, then how are sulcal/gyral landmarks taken into account? Thanks for any help! Tudor ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] surface-based morphometry registration
Thanks very much for explaining this Bruce. Tudor On 21 May 2014 22:01, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tudor 1. The smoothing we do is along the surface, so no matter how huge the kernel gets it only ever includes cortical gray matter. In contrast, volume smoothing kernels will happily smooth in white matter, skull, csf, the bore of the scanner, etc as the kernels get big. 2. Yes, we have a template, but it is a geometric one and not simply an average, so part of the advantage is higher dimensional nonlinear warping (which also exists in the volume), but part is that we register based on cortical folding patterns not image intensities, so folds are much more likely to align across subjects (and architectonic areas as well) cheers Bruce On Wed, 21 May 2014, Tudor Popescu wrote: Hi all, If I understand correctly, the surface-based morphometry (SBM) done by Freesurfer offers superior registration as compared to voxel-based methods such as VBM, in that: 1. SBM smoothing respects anatomical boundaries better than the 3D VBM smoothing. 2. SBM group analysis employs inter-subject alignment based on the patterns of sulci and gyri, as opposed to Talairach registration, which often ignores sulcal/gyral landmarks I'm not sure I understand those reasons, however. For 1., why does the smoothing operation (basically, a multiplication) care about anatomy or registration at all, such that it can be said it is better done in SBM vs VBM? And for 2., doesn't the Talairach registration used in VBM simply imply a certain target template? Surely such a template is used in SBM registration as well, and if that is the case, then how are sulcal/gyral landmarks taken into account? Thanks for any help! Tudor ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] mri_vol2vol memory error
Hello all, I am doing pre-processing for resting-state fMRI volumes, but I have encountered an error and am unsure of how to correct it: I have previously determined the nonlinear warping transformations from my subjects' anatomical (T1) space to the 2mm MNI template using ANTs. At the end of my pre-processing pipeline, I am trying to transform my subjects' functional volumes (206 TRs of 2sec) into this MNI space by 1) transforming the functional volumes into subject T1 space using mri_vol2vol, and 2) applying the nonlinear warp (from ANTs) to the volumes in subject-T1 space to ultimately have my subjects' functional data in MNI space. However, I am getting an error while running mri_vol2vol, where it cannot allocate region. I gather from looking around online that this is a memory issue, but I am not sure how to fix it. Thoughts? It is crucial that I be able to translate my functional data into common MNI space before performing second-level analyses... I do not encounter this issue when performing this transformation on functional connectivity maps (where I take an ROI defined in MNI space, transform it into T1, and then subject-EPI space, calculate the FC with the rest of the brain, and then invert the process by transforming back into T1, and finally MNI space). How can I get this to work with a larger file? Thank you in advance for your help, Ben Mooneyham -- Graduate Student UCSB - Department of Psychological Brain Sciences Building 429 Room 102 (210) 912-6076 bwmooney...@gmail.com ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Differing OS X version and recon-all
Hi, Wanted to check in about Mac OS X and any effects on recon-all that I may not be aware of. A while back the Mac was updated to 10.9.2 from some other version of 10.x.x. I ran half of my recon-all on 10.x.x, and am running my 2nd half on 10.9.2. The update was due to some IT person thinking the older version had security flaws. Will I need to rerun all of my subjects on 10.9.2, or has there been no reported differences between these two versions? Thanks, - Bryan ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal
Hi Yoonho - Tracula did not change at all between the 5.2 and 5.3 releases. It was recon-all that changed, and in fact 5.3 was released to correct a bug in 5.2, so it is not recommended to use 5.2 recon-all. For info about tracula versions, see: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates Hope this helps, a.y On Wed, 21 May 2014, Chung, Yoonho wrote: Hi Anastasia, I have a large set of freesurfer recons (T1) already processed through FS version 5.2 longitudinal stream while ago. However, I see now that there is an advantage of using Tracula 5.3 longitudinal stream for DTI longitudinal analysis. Do you know if I run the DWI data using 5.3 TRACULA longitudinal stream - if it will work with recons that are processed with 5.2? Thanks! Y ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] kvlQuantify naming problem [possible fix]
Thank you very much! We'll certainly fix this in the next release Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: C.P. Frost cpfr...@wisc.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, May 21, 2014 9:58:32 PM Subject: Re: [Freesurfer] kvlQuantify naming problem [possible fix] Follow-up: I then run into indexing problems when calling freeview with subfield volumes (similar to http://bit.ly/1pdEWRZ ), which leads me to believe kvlQuantify is the only script that relies on the old convention. Changing the names back to CA2_3.mgz, etc., fixes THAT problem. Rather than changing the filenames to the old convention, it's probably better to fix the script and leave the filenames alone. On Wed, May 21, 2014 at 1:06 PM, C.P. Frost car...@gmail.com wrote: Hello all, My site has recently upgraded to the newest version of Freesurfer, and I've run a set of subjects on recon-all using the hippocampal subfield segmentation flag. Everything went well. Then in running kvlQuantifyHippocampalSubfieldSegmentations.sh, I received error messages indicating that certain expected files didn't exist. In particular, among output files labeled with the scheme $subj/mri/posterior_$side_$struct.mgz, the script expected ...CA2-3.mgz and ...CA4-DG.mgz, and existing files were named ...CA2_3.mgz and ...CA4_DG.mgz -- in other words, the script expected a hyphen but instead the filenames contained an underscroe. After renaming the files appropriately, kvlQuantify... successfully generated the nonPartialVolumeStats files and everything worked fine. I didn't see any threads with this solution, and only one or two that mentioned the problem ( http://bit.ly/1vHbV5K ), so I thought I'd offer it up in case it could be addressed in a future release. Cheers, C.P. Frost ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_vol2vol memory error
mri_vol2vol when used in this way does not manage memory very well. It resamples the time series into a 256^3 volume of floats. Even for a small number of time points, this becomes unmanagebly huge On 05/21/2014 06:06 PM, Ben Mooneyham wrote: Hello all, I am doing pre-processing for resting-state fMRI volumes, but I have encountered an error and am unsure of how to correct it: I have previously determined the nonlinear warping transformations from my subjects' anatomical (T1) space to the 2mm MNI template using ANTs. At the end of my pre-processing pipeline, I am trying to transform my subjects' functional volumes (206 TRs of 2sec) into this MNI space by 1) transforming the functional volumes into subject T1 space using mri_vol2vol, and 2) applying the nonlinear warp (from ANTs) to the volumes in subject-T1 space to ultimately have my subjects' functional data in MNI space. However, I am getting an error while running mri_vol2vol, where it cannot allocate region. I gather from looking around online that this is a memory issue, but I am not sure how to fix it. Thoughts? It is crucial that I be able to translate my functional data into common MNI space before performing second-level analyses... I do not encounter this issue when performing this transformation on functional connectivity maps (where I take an ROI defined in MNI space, transform it into T1, and then subject-EPI space, calculate the FC with the rest of the brain, and then invert the process by transforming back into T1, and finally MNI space). How can I get this to work with a larger file? Thank you in advance for your help, Ben Mooneyham -- Graduate Student UCSB - Department of Psychological Brain Sciences Building 429 Room 102 (210) 912-6076 bwmooney...@gmail.com mailto:bwmooney...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] creating custom color table annotation file
Dear Freesurfer experts, Last week I asked a question about altering annotation and color tables so that I could plot groups of vertices that covaried together. I have figured out the solution to this, if anyone else is trying to do this too. You can read in an annotation file with the read_annotation.m function in Matlab. You can then edit the color table (a structure in Matlab) and then save the newly edited annotation file using write_annotation.m. I came across a couple of interesting issues when I was editing the colors and I was wondering if anyone knew the answers to them. 1. It looks like Freesurfer ultimately uses the decimal value for the specified color that is in the “label” variable. For example, if you wanted an all white brain, you would put in “16777215” in 163843 rows in 1 column in the variable “labels.” If you edit colortable.table, though this does not seem to affect anything. What is the purpose of corlortable.table if the label file overrides anything you put in the colortable.table? 2. I also noticed that the R G B values for colortable.table are backwards. To specify the correct color you have to enter it B G R. Does anyone know why this is the case? 3. Along those same lines, you need to enter the decimal color that is in the B G R order, not in R G B order. For example, if you enter 255, Freesurfer displays this as red, not blue. From what I researched, the correct decimal value for blue is 255. To get Freesurfer to display blue, you actually need to enter in 16711680, which is traditionally red. Why is this? I find it to be quite confusing. Perhaps these issues have already been discussed on the listserve, and if they have, could someone direct me to the discussion. I’ve looking through the archives extensively. Thank you so much for any suggestions you may have. Maria On Fri, May 16, 2014 at 4:02 PM, Maria Jalbrzikowski mjalbrzikow...@gmail.com wrote: Dear Freesurfer experts, I would like to get your help. I extracted cortical thickness values from each vertex from each of my individual subjects (example: path/subject_id/surf/lh.thickness.fsaverage.mgh). I then ran a covariance analysis over the whole group and identified modules or groups of vertices that covary together. The modules are given the names of colors. I end up with a module (color) assigned to each vertex. I now want to visualize this data (so I can if these module reflect specific neuroanatomical structures), but I'm not sure about how to do this. Does anyone know how to do this? I tried to make a new color table, with my different module colors as the structures. I don't know how to then incorporate this information so that I can view it. I've read the tutorials on the label and annotation files, but I have only become more confused. If anyone can help me with this problem, I'd be very greatful! Thank you, Maria -- Maria Jalbrzikowski, Ph.D. Department of Psychiatry Biobehavioral Sciences University of California, Los Angeles -- Maria Jalbrzikowski, Ph.D. Department of Psychiatry Biobehavioral Sciences University of California, Los Angeles ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] creating custom color table annotation file
Hi Maria I think we didn't realize there was any standard. As I remember, we do: r 16 + g 8 + b and stuff them into a 32 bit quantity cheers Bruce On Wed, 21 May 2014, Maria Jalbrzikowski wrote: Dear Freesurfer experts, Last week I asked a question about altering annotation and color tables so that I could plot groups of vertices that covaried together. I have figured out the solution to this, if anyone else is trying to do this too. You can read in an annotation file with the read_annotation.m function in Matlab. You can then edit the color table (a structure in Matlab) and then save the newly edited annotation file using write_annotation.m. I came across a couple of interesting issues when I was editing the colors and I was wondering if anyone knew the answers to them. 1. It looks like Freesurfer ultimately uses the decimal value for the specified color that is in the “label” variable. For example, if you wanted an all white brain, you would put in “16777215” in 163843 rows in 1 column in the variable “labels.” If you edit colortable.table, though this does not seem to affect anything. What is the purpose of corlortable.table if the label file overrides anything you put in the colortable.table? 2. I also noticed that the R G B values for colortable.table are backwards. To specify the correct color you have to enter it B G R. Does anyone know why this is the case? 3. Along those same lines, you need to enter the decimal color that is in the B G R order, not in R G B order. For example, if you enter 255, Freesurfer displays this as red, not blue. From what I researched, the correct decimal value for blue is 255. To get Freesurfer to display blue, you actually need to enter in 16711680, which is traditionally red. Why is this? I find it to be quite confusing. Perhaps these issues have already been discussed on the listserve, and if they have, could someone direct me to the discussion. I’ve looking through the archives extensively. Thank you so much for any suggestions you may have. Maria On Fri, May 16, 2014 at 4:02 PM, Maria Jalbrzikowski mjalbrzikow...@gmail.com wrote: Dear Freesurfer experts, I would like to get your help. I extracted cortical thickness values from each vertex from each of my individual subjects (example: path/subject_id/surf/lh.thickness.fsaverage.mgh). I then ran a covariance analysis over the whole group and identified modules or groups of vertices that covary together. The modules are given the names of colors. I end up with a module (color) assigned to each vertex. I now want to visualize this data (so I can if these module reflect specific neuroanatomical structures), but I'm not sure about how to do this. Does anyone know how to do this? I tried to make a new color table, with my different module colors as the structures. I don't know how to then incorporate this information so that I can view it. I've read the tutorials on the label and annotation files, but I have only become more confused. If anyone can help me with this problem, I'd be very greatful! Thank you, Maria -- Maria Jalbrzikowski, Ph.D. Department of Psychiatry Biobehavioral Sciences University of California, Los Angeles -- Maria Jalbrzikowski, Ph.D. Department of Psychiatry Biobehavioral Sciences University of California, Los Angeles ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] missing temporal lobes
Hi Eileen Does adding control points to both temporal lobes fix it? Cheers Bruce On May 20, 2014, at 9:34 AM, Daly, Eileen eileen.d...@kcl.ac.uk wrote: Hello all, We are having trouble with the output after running recon-all -all -subjid subjectx on our scans. Registrations and skull striping look okay, but the white matter and pial surface segmentations leave outportions of the anterior temporal lobe. After adding control points to the left temporal lobe, we then ran recon-all -autorecon2 –cp -autorecon3 -subjid subjects. This made the the left lobe look better, but then we spotted new missing bits on the right side anterior temporal lobe. Any ideas on dealing with these missing temporal lobe issues? Thanks, Eileen Daly ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] missing temporal lobes
Hi there, I tried to put more CP, so all the temporal lobe tissue is in the mask. This will end up in overestimation of white matter. So in a second step you will have to manually adjust WM mask. In my dataset, after adjusting WM mask, WM ist still little bit oversetimated, but at least i am not missing tissue. When you find a better option, I am glad to learn about. Good luck! Best, Kristina Von: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]quot; im Auftrag von quot;Bruce Fischl [fis...@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 22. Mai 2014 04:35 An: Freesurfer support list Betreff: Re: [Freesurfer] missing temporal lobes Hi Eileen Does adding control points to both temporal lobes fix it? Cheers Bruce On May 20, 2014, at 9:34 AM, Daly, Eileen eileen.d...@kcl.ac.uk wrote: Hello all, We are having trouble with the output after running recon-all -all -subjid subjectx on our scans. Registrations and skull striping look okay, but the white matter and pial surface segmentations leave outportions of the anterior temporal lobe. After adding control points to the left temporal lobe, we then ran recon-all -autorecon2 –cp -autorecon3 -subjid subjects. This made the the left lobe look better, but then we spotted new missing bits on the right side anterior temporal lobe. Any ideas on dealing with these missing temporal lobe issues? Thanks, Eileen Daly ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
