I usually use this little bash script (named myrecon) to process my images.
#!/bin/bash mkdir ~/freesurfer/subjects/$1/mri/orig -p cp ~/freesurfer/ImgOrig/$1/* ~/freesurfer/subjects/$1/mri/orig/ recon-all -all -s $1 -cw256 -hippo-subfields -qcache With this script I get the entire -all pipeline, plus hippocampal segmentation and the cache for posterior analysis with qdec. All in a once and just typing myrecon subject. You can check if the hippo-subfields were correctly processed reading the recon-all-status.log and with more detail reading hippo-subfields.log. Both files are in freesurfer/subjects/yoursubject/scripts. I attached one of my recon-all-status.log so you can compare. The last line is related to hippo-subfields processing. After recon-all you will see several posterior*.mgz files inside freesurfer/subjects/yoursubject/mri/. BTW, ImgOrig is a custom folder where I have one folder for each subject with the original 00X.mgz file(s). Marcos Em Seg, 2013-05-27 às 09:45 -0700, Salil Soman escreveu: > I can add that running the -hippo-subfields flag separately did work: > > recon-all -s SUBJECTIDENTIFIER -hippo-subfields > > > Is there a reason the order of processing should matter? Is there a > way I can change my recon-all call (below) so that hippo-subfields > will get processed (so I do not have to make a separate call)? > > recon-all -i SPGR/*.gz -s SUBJECTIDENTIFIER -nuintensitycor-3T > -nocanorm -openmp 50 -hippo-subfields -all > > > Thank you, > > Sal > > > > > > > > On Sun, May 26, 2013 at 2:33 PM, Salil Soman <salso...@stanford.edu> > wrote: > > Dear Freesurfer Experts, > > > I have been running freesurfer 5.3 without any reported errors > using the following command: > > recon-all -i SPGR/*.gz -s SUBJECTIDENTIFIER -nuintensitycor-3T > -nocanorm -openmp 50 -hippo-subfields -all > > > However, when I look for any of the hippocampal subfield stats > (as described on > > http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation), I do > not find any of them. > > > Any suggestions on what I am doing incorrectly? > > Best wishes, > > Salil Soman, MD, MS > > > > > > > _______________________________________________ > 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.
status file for recon-all Thu May 23 01:32:10 BRT 2013 #@# MotionCor Thu May 23 01:32:10 BRT 2013 #@# Talairach Thu May 23 01:35:39 BRT 2013 #@# Talairach Failure Detection Thu May 23 01:37:16 BRT 2013 #@# Nu Intensity Correction Thu May 23 01:37:16 BRT 2013 #@# Intensity Normalization Thu May 23 01:38:35 BRT 2013 #@# Skull Stripping Thu May 23 01:41:00 BRT 2013 #@# EM Registration Thu May 23 02:16:10 BRT 2013 #@# CA Normalize Thu May 23 02:42:59 BRT 2013 #@# CA Reg Thu May 23 02:44:52 BRT 2013 #@# CA Reg Inv Thu May 23 07:28:41 BRT 2013 #@# Remove Neck Thu May 23 07:29:49 BRT 2013 #@# SkullLTA Thu May 23 07:30:59 BRT 2013 #@# SubCort Seg Thu May 23 08:02:06 BRT 2013 #@# Merge ASeg Thu May 23 08:23:51 BRT 2013 #@# Intensity Normalization2 Thu May 23 08:23:51 BRT 2013 #@# Mask BFS Thu May 23 08:28:03 BRT 2013 #@# WM Segmentation Thu May 23 08:28:06 BRT 2013 #@# Fill Thu May 23 08:31:06 BRT 2013 #@# Tessellate lh Thu May 23 08:32:01 BRT 2013 #@# Smooth1 lh Thu May 23 08:32:09 BRT 2013 #@# Inflation1 lh Thu May 23 08:32:14 BRT 2013 #@# QSphere lh Thu May 23 08:32:50 BRT 2013 #@# Fix Topology lh Thu May 23 08:37:40 BRT 2013 #@# Make White Surf lh Thu May 23 09:03:51 BRT 2013 #@# Smooth2 lh Thu May 23 09:10:51 BRT 2013 #@# Inflation2 lh Thu May 23 09:10:55 BRT 2013 #@# Curvature Stats lh Thu May 23 09:13:12 BRT 2013 #@# Sphere lh Thu May 23 09:13:16 BRT 2013 #@# Surf Reg lh Thu May 23 10:08:23 BRT 2013 #@# Jacobian white lh Thu May 23 10:45:12 BRT 2013 #@# AvgCurv lh Thu May 23 10:45:15 BRT 2013 #@# Cortical Parc lh Thu May 23 10:45:17 BRT 2013 #@# Make Pial Surf lh Thu May 23 10:46:15 BRT 2013 #@# Surf Volume lh Thu May 23 11:00:00 BRT 2013 #@# WM/GM Contrast lh Thu May 23 11:00:00 BRT 2013 #@# Parcellation Stats lh Thu May 23 11:00:11 BRT 2013 #@# Cortical Parc 2 lh Thu May 23 11:00:32 BRT 2013 #@# Parcellation Stats 2 lh Thu May 23 11:01:36 BRT 2013 #@# Cortical Parc 3 lh Thu May 23 11:01:56 BRT 2013 #@# Parcellation Stats 3 lh Thu May 23 11:02:52 BRT 2013 #@# Tessellate rh Thu May 23 11:03:09 BRT 2013 #@# Smooth1 rh Thu May 23 11:03:18 BRT 2013 #@# Inflation1 rh Thu May 23 11:03:22 BRT 2013 #@# QSphere rh Thu May 23 11:04:00 BRT 2013 #@# Fix Topology rh Thu May 23 11:08:59 BRT 2013 #@# Make White Surf rh Thu May 23 11:35:17 BRT 2013 #@# Smooth2 rh Thu May 23 11:41:58 BRT 2013 #@# Inflation2 rh Thu May 23 11:42:02 BRT 2013 #@# Curvature Stats rh Thu May 23 11:44:14 BRT 2013 #@# Sphere rh Thu May 23 11:44:19 BRT 2013 #@# Surf Reg rh Thu May 23 12:54:31 BRT 2013 #@# Jacobian white rh Thu May 23 13:43:36 BRT 2013 #@# AvgCurv rh Thu May 23 13:43:38 BRT 2013 #@# Cortical Parc rh Thu May 23 13:43:40 BRT 2013 #@# Make Pial Surf rh Thu May 23 13:44:39 BRT 2013 #@# Surf Volume rh Thu May 23 13:58:19 BRT 2013 #@# WM/GM Contrast rh Thu May 23 13:58:19 BRT 2013 #@# Parcellation Stats rh Thu May 23 13:58:29 BRT 2013 #@# Cortical Parc 2 rh Thu May 23 13:58:52 BRT 2013 #@# Parcellation Stats 2 rh Thu May 23 13:59:59 BRT 2013 #@# Cortical Parc 3 rh Thu May 23 14:00:22 BRT 2013 #@# Parcellation Stats 3 rh Thu May 23 14:01:21 BRT 2013 #@# Cortical ribbon mask Thu May 23 14:01:41 BRT 2013 #@# ASeg Stats Thu May 23 14:22:04 BRT 2013 #@# AParc-to-ASeg Thu May 23 14:26:36 BRT 2013 #@# WMParc Thu May 23 14:31:21 BRT 2013 #@# Qdec Cache lh thickness fsaverage Thu May 23 14:44:27 BRT 2013 #@# Qdec Cache lh thickness fwhm0 fsaverage Thu May 23 14:44:34 BRT 2013 #@# Qdec Cache lh thickness fwhm5 fsaverage Thu May 23 14:44:37 BRT 2013 #@# Qdec Cache lh thickness fwhm10 fsaverage Thu May 23 14:44:43 BRT 2013 #@# Qdec Cache lh thickness fwhm15 fsaverage Thu May 23 14:44:49 BRT 2013 #@# Qdec Cache lh thickness fwhm20 fsaverage Thu May 23 14:44:56 BRT 2013 #@# Qdec Cache lh thickness fwhm25 fsaverage Thu May 23 14:45:03 BRT 2013 #@# Qdec Cache lh area fsaverage Thu May 23 14:45:11 BRT 2013 #@# Qdec Cache lh area fwhm0 fsaverage Thu May 23 14:45:20 BRT 2013 #@# Qdec Cache lh area fwhm5 fsaverage Thu May 23 14:45:23 BRT 2013 #@# Qdec Cache lh area fwhm10 fsaverage Thu May 23 14:45:29 BRT 2013 #@# Qdec Cache lh area fwhm15 fsaverage Thu May 23 14:45:35 BRT 2013 #@# Qdec Cache lh area fwhm20 fsaverage Thu May 23 14:45:42 BRT 2013 #@# Qdec Cache lh area fwhm25 fsaverage Thu May 23 14:45:49 BRT 2013 #@# Qdec Cache lh area.pial fsaverage Thu May 23 14:45:57 BRT 2013 #@# Qdec Cache lh area.pial fwhm0 fsaverage Thu May 23 14:46:06 BRT 2013 #@# Qdec Cache lh area.pial fwhm5 fsaverage Thu May 23 14:46:09 BRT 2013 #@# Qdec Cache lh area.pial fwhm10 fsaverage Thu May 23 14:46:15 BRT 2013 #@# Qdec Cache lh area.pial fwhm15 fsaverage Thu May 23 14:46:21 BRT 2013 #@# Qdec Cache lh area.pial fwhm20 fsaverage Thu May 23 14:46:28 BRT 2013 #@# Qdec Cache lh area.pial fwhm25 fsaverage Thu May 23 14:46:35 BRT 2013 #@# Qdec Cache lh volume fsaverage Thu May 23 14:46:43 BRT 2013 #@# Qdec Cache lh volume fwhm0 fsaverage Thu May 23 14:46:53 BRT 2013 #@# Qdec Cache lh volume fwhm5 fsaverage Thu May 23 14:46:55 BRT 2013 #@# Qdec Cache lh volume fwhm10 fsaverage Thu May 23 14:47:01 BRT 2013 #@# Qdec Cache lh volume fwhm15 fsaverage Thu May 23 14:47:08 BRT 2013 #@# Qdec Cache lh volume fwhm20 fsaverage Thu May 23 14:47:14 BRT 2013 #@# Qdec Cache lh volume fwhm25 fsaverage Thu May 23 14:47:21 BRT 2013 #@# Qdec Cache lh curv fsaverage Thu May 23 14:47:29 BRT 2013 #@# Qdec Cache lh curv fwhm0 fsaverage Thu May 23 14:47:36 BRT 2013 #@# Qdec Cache lh curv fwhm5 fsaverage Thu May 23 14:47:39 BRT 2013 #@# Qdec Cache lh curv fwhm10 fsaverage Thu May 23 14:47:45 BRT 2013 #@# Qdec Cache lh curv fwhm15 fsaverage Thu May 23 14:47:51 BRT 2013 #@# Qdec Cache lh curv fwhm20 fsaverage Thu May 23 14:47:58 BRT 2013 #@# Qdec Cache lh curv fwhm25 fsaverage Thu May 23 14:48:05 BRT 2013 #@# Qdec Cache lh sulc fsaverage Thu May 23 14:48:13 BRT 2013 #@# Qdec Cache lh sulc fwhm0 fsaverage Thu May 23 14:48:20 BRT 2013 #@# Qdec Cache lh sulc fwhm5 fsaverage Thu May 23 14:48:23 BRT 2013 #@# Qdec Cache lh sulc fwhm10 fsaverage Thu May 23 14:48:29 BRT 2013 #@# Qdec Cache lh sulc fwhm15 fsaverage Thu May 23 14:48:35 BRT 2013 #@# Qdec Cache lh sulc fwhm20 fsaverage Thu May 23 14:48:42 BRT 2013 #@# Qdec Cache lh sulc fwhm25 fsaverage Thu May 23 14:48:49 BRT 2013 #@# Qdec Cache lh white.K fsaverage Thu May 23 14:48:57 BRT 2013 #@# Qdec Cache lh white.H fsaverage Thu May 23 14:48:57 BRT 2013 #@# Qdec Cache lh jacobian_white fsaverage Thu May 23 14:48:57 BRT 2013 #@# Qdec Cache lh jacobian_white fwhm0 fsaverage Thu May 23 14:49:04 BRT 2013 #@# Qdec Cache lh jacobian_white fwhm5 fsaverage Thu May 23 14:49:07 BRT 2013 #@# Qdec Cache lh jacobian_white fwhm10 fsaverage Thu May 23 14:49:13 BRT 2013 #@# Qdec Cache lh jacobian_white fwhm15 fsaverage Thu May 23 14:49:19 BRT 2013 #@# Qdec Cache lh jacobian_white fwhm20 fsaverage Thu May 23 14:49:26 BRT 2013 #@# Qdec Cache lh jacobian_white fwhm25 fsaverage Thu May 23 14:49:33 BRT 2013 #@# Qdec Cache lh w-g.pct.mgh fsaverage Thu May 23 14:49:41 BRT 2013 #@# Qdec Cache lh w-g.pct.mgh fwhm0 fsaverage Thu May 23 14:49:48 BRT 2013 #@# Qdec Cache lh w-g.pct.mgh fwhm5 fsaverage Thu May 23 14:49:51 BRT 2013 #@# Qdec Cache lh w-g.pct.mgh fwhm10 fsaverage Thu May 23 14:49:57 BRT 2013 #@# Qdec Cache lh w-g.pct.mgh fwhm15 fsaverage Thu May 23 14:50:03 BRT 2013 #@# Qdec Cache lh w-g.pct.mgh fwhm20 fsaverage Thu May 23 14:50:10 BRT 2013 #@# Qdec Cache lh w-g.pct.mgh fwhm25 fsaverage Thu May 23 14:50:17 BRT 2013 #@# Qdec Cache rh thickness fsaverage Thu May 23 14:50:25 BRT 2013 #@# Qdec Cache rh thickness fwhm0 fsaverage Thu May 23 14:50:32 BRT 2013 #@# Qdec Cache rh thickness fwhm5 fsaverage Thu May 23 14:50:35 BRT 2013 #@# Qdec Cache rh thickness fwhm10 fsaverage Thu May 23 14:50:41 BRT 2013 #@# Qdec Cache rh thickness fwhm15 fsaverage Thu May 23 14:50:47 BRT 2013 #@# Qdec Cache rh thickness fwhm20 fsaverage Thu May 23 14:50:54 BRT 2013 #@# Qdec Cache rh thickness fwhm25 fsaverage Thu May 23 14:51:01 BRT 2013 #@# Qdec Cache rh area fsaverage Thu May 23 14:51:08 BRT 2013 #@# Qdec Cache rh area fwhm0 fsaverage Thu May 23 14:51:18 BRT 2013 #@# Qdec Cache rh area fwhm5 fsaverage Thu May 23 14:51:21 BRT 2013 #@# Qdec Cache rh area fwhm10 fsaverage Thu May 23 14:51:27 BRT 2013 #@# Qdec Cache rh area fwhm15 fsaverage Thu May 23 14:51:33 BRT 2013 #@# Qdec Cache rh area fwhm20 fsaverage Thu May 23 14:51:40 BRT 2013 #@# Qdec Cache rh area fwhm25 fsaverage Thu May 23 14:51:47 BRT 2013 #@# Qdec Cache rh area.pial fsaverage Thu May 23 14:51:55 BRT 2013 #@# Qdec Cache rh area.pial fwhm0 fsaverage Thu May 23 14:52:04 BRT 2013 #@# Qdec Cache rh area.pial fwhm5 fsaverage Thu May 23 14:52:07 BRT 2013 #@# Qdec Cache rh area.pial fwhm10 fsaverage Thu May 23 14:52:13 BRT 2013 #@# Qdec Cache rh area.pial fwhm15 fsaverage Thu May 23 14:52:19 BRT 2013 #@# Qdec Cache rh area.pial fwhm20 fsaverage Thu May 23 14:52:26 BRT 2013 #@# Qdec Cache rh area.pial fwhm25 fsaverage Thu May 23 14:52:33 BRT 2013 #@# Qdec Cache rh volume fsaverage Thu May 23 14:52:41 BRT 2013 #@# Qdec Cache rh volume fwhm0 fsaverage Thu May 23 14:52:51 BRT 2013 #@# Qdec Cache rh volume fwhm5 fsaverage Thu May 23 14:52:53 BRT 2013 #@# Qdec Cache rh volume fwhm10 fsaverage Thu May 23 14:52:59 BRT 2013 #@# Qdec Cache rh volume fwhm15 fsaverage Thu May 23 14:53:06 BRT 2013 #@# Qdec Cache rh volume fwhm20 fsaverage Thu May 23 14:53:12 BRT 2013 #@# Qdec Cache rh volume fwhm25 fsaverage Thu May 23 14:53:19 BRT 2013 #@# Qdec Cache rh curv fsaverage Thu May 23 14:53:27 BRT 2013 #@# Qdec Cache rh curv fwhm0 fsaverage Thu May 23 14:53:34 BRT 2013 #@# Qdec Cache rh curv fwhm5 fsaverage Thu May 23 14:53:37 BRT 2013 #@# Qdec Cache rh curv fwhm10 fsaverage Thu May 23 14:53:43 BRT 2013 #@# Qdec Cache rh curv fwhm15 fsaverage Thu May 23 14:53:49 BRT 2013 #@# Qdec Cache rh curv fwhm20 fsaverage Thu May 23 14:53:56 BRT 2013 #@# Qdec Cache rh curv fwhm25 fsaverage Thu May 23 14:54:03 BRT 2013 #@# Qdec Cache rh sulc fsaverage Thu May 23 14:54:11 BRT 2013 #@# Qdec Cache rh sulc fwhm0 fsaverage Thu May 23 14:54:18 BRT 2013 #@# Qdec Cache rh sulc fwhm5 fsaverage Thu May 23 14:54:21 BRT 2013 #@# Qdec Cache rh sulc fwhm10 fsaverage Thu May 23 14:54:27 BRT 2013 #@# Qdec Cache rh sulc fwhm15 fsaverage Thu May 23 14:54:34 BRT 2013 #@# Qdec Cache rh sulc fwhm20 fsaverage Thu May 23 14:54:40 BRT 2013 #@# Qdec Cache rh sulc fwhm25 fsaverage Thu May 23 14:54:47 BRT 2013 #@# Qdec Cache rh white.K fsaverage Thu May 23 14:54:55 BRT 2013 #@# Qdec Cache rh white.H fsaverage Thu May 23 14:54:55 BRT 2013 #@# Qdec Cache rh jacobian_white fsaverage Thu May 23 14:54:55 BRT 2013 #@# Qdec Cache rh jacobian_white fwhm0 fsaverage Thu May 23 14:55:02 BRT 2013 #@# Qdec Cache rh jacobian_white fwhm5 fsaverage Thu May 23 14:55:05 BRT 2013 #@# Qdec Cache rh jacobian_white fwhm10 fsaverage Thu May 23 14:55:11 BRT 2013 #@# Qdec Cache rh jacobian_white fwhm15 fsaverage Thu May 23 14:55:17 BRT 2013 #@# Qdec Cache rh jacobian_white fwhm20 fsaverage Thu May 23 14:55:24 BRT 2013 #@# Qdec Cache rh jacobian_white fwhm25 fsaverage Thu May 23 14:55:31 BRT 2013 #@# Qdec Cache rh w-g.pct.mgh fsaverage Thu May 23 14:55:39 BRT 2013 #@# Qdec Cache rh w-g.pct.mgh fwhm0 fsaverage Thu May 23 14:55:46 BRT 2013 #@# Qdec Cache rh w-g.pct.mgh fwhm5 fsaverage Thu May 23 14:55:49 BRT 2013 #@# Qdec Cache rh w-g.pct.mgh fwhm10 fsaverage Thu May 23 14:55:55 BRT 2013 #@# Qdec Cache rh w-g.pct.mgh fwhm15 fsaverage Thu May 23 14:56:01 BRT 2013 #@# Qdec Cache rh w-g.pct.mgh fwhm20 fsaverage Thu May 23 14:56:08 BRT 2013 #@# Qdec Cache rh w-g.pct.mgh fwhm25 fsaverage Thu May 23 14:56:15 BRT 2013 #@# BA Labels lh Thu May 23 14:56:23 BRT 2013 #@# BA Labels rh Thu May 23 15:00:37 BRT 2013 #@# Ex-vivo Entorhinal Cortex Label lh Thu May 23 15:04:52 BRT 2013 #@# Ex-vivo Entorhinal Cortex Label rh Thu May 23 15:05:08 BRT 2013 #@# Hippocampal Subfields processing Thu May 23 15:05:24 BRT 2013 recon-all -s suj1 finished without error at Thu May 23 17:49:36 BRT 2013
_______________________________________________ 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.
