[Freesurfer] help with using optseq2
Hello, I'm trying to create trial sequences for a slow event related fMRI experiment. I have 10 classes of stimuli, and each stimulus lasts 5 sec and repeats twice in a run. Environment: Linux 3.13.0-35-generic #62-Ubuntu SMP UTC 2014 x86_64 x86_64 x86_64 GNU/Linux I ran: ./optseq2 --ntp 144 --tr 2.5 \ --ev evt1 5 2 --ev evt2 5 2 --ev evt3 5 2 --ev evt4 5 2 --ev evt5 5 2 --ev evt6 5 2 --ev evt7 5 2 --ev evt8 5 2 --ev evt9 5 2 --ev evt10 5 2 \ --nkeep 10 --psdwin 0 20 --o exp_video \ --tnullmax 25 --tnullmin 7.5 \ --nsearch 1 Almost all of the sequences have extremely long NULL at the end of a run, like 82.5sec (please see one of sequences below). I am aware that optseq2 is for rapid event related fMRI, and wonder if the problem is due to specific parameters of my design, or due to a bug. I would appreciate any comments or help. Thank you very much! Best regards, Heeyoung 0.55.000 1. evt5 5.07.500 1. NULL 12.500095.000 1. evt9 17.500007.500 1. NULL 25.35.000 1. evt3 30.07.500 1. NULL 37.5000 105.000 1. evt10 42.50000 12.500 1. NULL 55.75.000 1. evt7 60.0 10.000 1. NULL 70.35.000 1. evt3 75.07.500 1. NULL 82.500045.000 1. evt4 87.50000 15.000 1. NULL 102.500065.000 1. evt6 107.500007.500 1. NULL 115.65.000 1. evt6 120.0 10.000 1. NULL 130.85.000 1. evt8 135.0 17.500 1. NULL 152.500015.000 1. evt1 157.500007.500 1. NULL 165.25.000 1. evt2 170.07.500 1. NULL 177.5000 105.000 1. evt10 182.500007.500 1. NULL 190.85.000 1. evt8 195.07.500 1. NULL 202.500095.000 1. evt9 207.50000 12.500 1. NULL 220.45.000 1. evt4 225.07.500 1. NULL 232.500075.000 1. evt7 237.500007.500 1. NULL 245.15.000 1. evt1 250.07.500 1. NULL 257.500055.000 1. evt5 262.50000 10.000 1. NULL 272.500025.000 1. evt2 277.50000 82.500 1. NULL ___ 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] Regarding: Qdec GLM design error
Dear freesurfer experts, I am new to Qdec analysis and I trying to do( using the information provided in the qdec wiki page) group surface analysis in SCA patients 1and 2 and compare their surface thickness using qdec command. The data table is loading successfully but when I go the design and click on When I click on the Analyze button (this is after I changed the Untilted folder to the lh-thickess-10), I am getting the following error: ERROR: QdecGlmDesign::Create: could not create directory /usr/local/freesurfer/subjects/qdec/lh-thic k ness-10 For display purposes, I put the average subject included in SUBJECTS_DIR which is in /home/anup/Desktop/freesurfer_processed/qdec, with the following bash command: if [ ! -e fsaverage ]; then ln -s $FREESURFER_HOME/subjects/fsaverage; fi I have Discrete facrors: Gender (Male and Female) and Diagnosis (divided into SCA1 and SCA2) and Continous factors: Age, CAG repeat, lh-thickness and rh-thickness. Will you please let me know where am I going wrong? Any help will be forever appreciated! Thanks and regards, Sampada ___ 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] Tksurfer and Tkregister2 in Ubuntu 14.04
Hi Zeke, I am wondering if you had a chance to look at this. Thanks, Reza Hello Reza, I wasn't able to replicate on Ubuntu 12 but it's entirely possible this but exists only in Ubuntu 14. It's tough because we don't have test machines with every Linux distro that people post to the list about in order to attempt replicate. But I'll install Ubuntu 14 on a laptop after OHBM concludes and investigate. -Zeke On Friday, June 12, 2015, Reza Rajimehr rajim...@gmail.com javascript:_e(%7B%7D,'cvml','rajim...@gmail.com'); wrote: Hi Bruce, I guess I will eventually move to freeview - though I am not quite sure if it is easy to use with FS-FAST. For now, all features of tksurfer/tkmedit/tkregister2 work fine for me, except the one described below. So it would be great if this bug, that is specific for ubuntu, is resolved. Best, Reza Hi Reza can you use freeview for what you want instead? tksurfer and tkmedit are deprecated cheers Bruce On Thursday, June 11, 2015, Reza Rajimehr rajim...@gmail.com wrote: Hi, Is there any plan by the Freesurfer team to address this well-known bug? http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35938.html http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36193.html For now the only workaround is to enter values through command-line. Best, Reza ___ 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] help
I am very new to Freesurfer and are having problems getting it up and running. I have followed, successfully the set up and configuration instructions up the license. At this point, after entering the license information received in the email I try and to exit and save and I get a message that reads error writing license.txt: Permission Denied. However, we were able to run the Test your FreeSurfer Installation part successfully. But when we try to work with our own MRI scans, we receive a whole bunch of error message such as: mkdir: //Application/freesurfer/subjects/subj001: Permission denied I am guessing this is due to license.txt. How can I resolve this? Karen Karen Bunday, PhD Honorary Research Associate Sobell Department of Motor Neuroscience and Movement Disorders Institute of Neurology, University College London 33 Queen Square London WC1N 3BG ___ 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] help
As the error message indicates, this is a permissions issue. To solve the license problem, your best bet is to create the license files in your home directory (or anywhere you have adequate permissions) and copy it to /Applications/freesurfer. This is described in a little more detail in the License section on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac Your subjects dir issue is essentially the same problem. The default SUBJECTS_DIR (/Application/freesurfer/subjects) is write protected. So either place the subject data somewhere you adequate permissions, and set the SUBJECTS_DIR accordingly, or open up the permissions if the default SUBJECTS_DIR using the following coomand: $ sudo chmod -R a+w /Applications/freesurfer Cheers, -Zeke I am very new to Freesurfer and are having problems getting it up and running. I have followed, successfully the set up and configuration instructions up the license. At this point, after entering the license information received in the email I try and to exit and save and I get a message that reads error writing license.txt: Permission Denied. However, we were able to run the Test your FreeSurfer Installation part successfully. But when we try to work with our own MRI scans, we receive a whole bunch of error message such as: mkdir: //Application/freesurfer/subjects/subj001: Permission denied I am guessing this is due to license.txt. How can I resolve this? Karen Karen Bunday, PhD Honorary Research Associate Sobell Department of Motor Neuroscience and Movement Disorders Institute of Neurology, University College London 33 Queen Square London WC1N 3BG ___ 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] (no subject)
Hi FS, MR images of two of my subjects in a group have been acquired with different T1 protocol from the rest. All the subjects has been acquired with sagittal 1mm iso : Width: 230.00 mm (256) Height: 230.00 mm (256) Resolution: 1.113 pixels per mm Pixel size: 0.90x0.90 mm and these two with coronal iso: Width: 220.00 mm (256) Height: 220.00 mm (256) Resolution: 1.164 pixels per mm Pixel size: 0.86x0.86 mm Now I want to use these images in group analyses with Q-dec. Does Freesurfer Freesurfer automatically reformat/reconstruct the T1 images independent of their acquisition protocol? OR Do I need to reformat the images before running recon-all and then use in the Qdec? If so, which program do you recommend to use? Best regards, Amirhossein Manzouri ___ 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] (no subject)
Hi Amirhossein we will reformat them all to 1mm iso during recon-all. Hopefully those differences are small enough not to cause a bias. cheers Bruce On Thu, 16 Jul 2015, amirhossein manzouri wrote: Hi FS, MR images of two of my subjects in a group have been acquired with different T1 protocol from the rest. All the subjects has been acquired with sagittal 1mm iso : Width: 230.00 mm (256) Height: 230.00 mm (256) Resolution: 1.113 pixels per mm Pixel size: 0.90x0.90 mm and these two with coronal iso: Width: 220.00 mm (256) Height: 220.00 mm (256) Resolution: 1.164 pixels per mm Pixel size: 0.86x0.86 mm Now I want to use these images in group analyses with Q-dec. Does Freesurfer Freesurfer automatically reformat/reconstruct the T1 images independent of their acquisition protocol? OR Do I need to reformat the images before running recon-all and then use in the Qdec? If so, which program do you recommend to use? Best regards, Amirhossein Manzouri ___ 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] tracula reinit failure filled my hard drive
Hi, I'm using freesurfer-Darwin-lion-stable-pub-v5.3.0 and the latest version of tracula (downloaded Sept 2014). I was running 'trac-all -prior -c mydmrircfile.txt' with reinit=1 on a few tracts that initially reconstructed to look like single voxels. The log file indicated there was difficulty converging on a solution: INFO: Distances between consecutive points are 12 12 13 14 INFO: Selected control points in test subject's space are 161 100 154 163 104 142 159 105 130 159 101 117 160 91 107 INFO: Distances between consecutive points in test subject's space are 13 13 14 14 WARN: Could not find satisfactory control point fit - try 1435 Finding center streamline INFO: Step is 3 voxels WARN: Turning off deviation check for center streamline INFO: Step is 3 voxels WARN: Turning off FA check for center streamline INFO: Step is 3 voxels WARN: Turning off overlap check for center streamline INFO: Step is 3 voxels WARN: Turning off overlap check for center streamline The rest of the 50 GB file is the same last 2 Info and Warn lines. I was also sending the terminal output to a log file. So, it too contains 50GB of Info and Warn lines. It wasn't a very large hard drive to start with, but this did end up leaving the drive with 0 bytes of free space, which also caused the processes trying to write to the disk at the time to eventually crash (after reporting there is no space left on device, many times). The tracts in question probably won't reconstruct well. But if you have time for a feature request, maybe you could detect that it hasn't or won't converge at this point? Thanks, Peggy ___ 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] where to start recon-all after edits
Hi, If the surfaces are 'done' and we update/edit the the aseg.mgz with recon-all -surfsegedit and then run recon-all -autorecon2-cp -autorecon3 to update the .stats, this also creates new wm and pial surfaces that may be different to those used for -surfsegedit. Is that right? As another alternative, could we run say, recon-all -autorecon2-cp_ -autorecon3_ that have set DoWhiteSurfs = 0; set DoPialSurfs = 0; so that new surfaces are not created and avoid needing to recheck the wm/pial surfaces (as they were previously considered done) as well as being the same as those used for the -surfsegedit. Looking forward to a reply, thanks, P On Mon, 18 May 2015 16:27:31 -0700 prasser lt;pras...@zoho.comgt; wrote Hi, This is a repost, hope someone can please comment? Thanks. On Wed, 06 May 2015 00:07:17 -0700 prasser lt;pras...@zoho.comgt; wrote Thanks Martin. The concern I have with using -autorecon2-cp -autorecon3 after -surfsegedit is that, new surfaces are created during -autorecon2-cp -autorecon3 so that aseg and the surfaces are always out of step with each other. Any suggestions on how I could test the validity of the method described here as an alternative: recon-all -surfsegedit then edit aseg if needed and then: recon-all -aparc2aseg -segstats -wmparc On Tue, 05 May 2015 07:09:48 -0700 Martin Reuter lt;mreu...@nmr.mgh.harvard.edugt; wrote Yes, if this is in the long, you also need to add the -long …. stuff Martin On Apr 28, 2015, at 12:46 AM, prasser lt;pras...@zoho.comgt; wrote: Thanks for your response, not sure if I've quite got it yet. So, after the surfaces are done and we update/edit the the aseg.mgz with say, recon-all -surfsegedit we need to re-run recon-all -autorecon2-cp -autorecon3 On Thu, 23 Apr 2015 06:45:00 -0700 Bruce Fischl lt;fis...@nmr.mgh.harvard.edugt; wrote I would think autorecon2-cp autorecon3 would be fine, but maybe Martin can comment? On Wed, 22 Apr 2015, prasser wrote: gt; Repost.Thanks. gt; gt; gt; On Mon, 20 Apr 2015 16:35:29 -0700 lt;pras...@zoho.comgt; wrote gt; gt; Thank you again for your reply. gt; gt; For editing aseg.mgz, as mentioned in gt; gt; https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegme gt; ntations gt; gt; it does suggest using -autorecon2-noaseg, but from what I can see this does not gt; update the aparc+aseg.mgz and associated .stats etc is that correct? Doesn't gt; this command (as does -autorecon3) also re-create surfaces that would need to be gt; re-checked and re-edited if needed? gt; gt; Also, I think FS5.1 does not have the -autorecon2-noaseg flag. gt; gt; As an alternative, with completed wm/pial boundaries could we run gt; gt; recon-all -surfsegedit, gt; gt; then we would edit aseg as needed and then: gt; gt; recon-all -aparc2aseg -segstats -wmparc gt; gt; This will not change any surfaces but would update aseg.stats gt; aparc.a2009s+aseg.mgz wmparc.mgz wmparc.stats etc gt; gt; P gt; gt; gt; On Mon, 20 Apr 2015 13:42:49 -0700 Martin gt; Reuterlt;mreu...@nmr.mgh.harvard.edugt; wrote gt; Hi gt; gt; so take a look at gt; https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData gt; where the entry points are described ( for brainmask and finalsurfs gt; -autorecon-pial should be OK, for aseg it says to use gt; gt; -autorecon2-noaseg ) gt; Also this page gt; https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags gt; has details on the steps. gt; gt; Best, Martin gt; gt; gt; gt; On 04/20/2015 03:21 PM, Martin Reuter wrote: gt; gt; usually edits to surfaces should not be required in the long. The gt; surfaces there get initialized from the base, so you need to make gt; sure the base surface is as accurate as possible. Several edits also gt; get transferred automatically from the cross sectional runs. See gt; this gt; http://freesurfer.net/fswiki/LongitudinalEdits gt; for a description of the different edits, and where they should be gt; done. gt; gt; About where to restart after making the edits, everything should be gt; done the same way as in the regular (cross sectional) processing. gt; So you specifically ask about: gt; - brainmask edits gt; - brainfinalsurf edits gt; - and manual aseg edits. gt; gt; I just looked at the description of those regular edits gt; http://freesurfer.net/fswiki/Edits gt; but sadly there it does not say where to start re-run either. I'll gt; try to find out and update that soon. gt; gt; I hope someone with editing experience can chime in and tell us. (I gt; changed the subject, so that it get's read). gt; gt; Cheers, Martin gt; gt; On 04/20/2015 09:44 AM, Bruce Fischl wrote: gt; gt; cheers gt; Bruce gt; gt; gt; On Mon, 20 Apr 2015, prasser wrote: gt; gt; Dear All, gt; I wanted to check that corrections to a Long pial gt;
[Freesurfer] mri_vol2vol
Hi Freesurfer experts,
We are analyzing data for a simultaneous PET-MRI study, and are having trouble
registering individual subject BPnd maps to fsaverage space. I attached a photo
of a post-registration subject (the left side is cut off). I had previously
registered each individual BPnd volume map to the subject's volume space using
bbregister (naming the reg file register{subject}.dat), and then transformed
them into a new volume file using the mri_vol2vol command, and referencing the
file generated by bbregister.
This is the command I used:
mri_vol2vol --mov
$SUBJECTS_DIR/NNC_PMOD_LoganRef_BPnd/fs_NNC112_0045_RBV_MC_s10v3_LoganRef_BPnd.nii
(**this is the original volume file**) --fstarg --reg register0045.dat --o
$SUBJECTS_DIR/NNC_PMOD_LoganRef_BPnd/fs_NNC112_0045_RBV_MC_s10v3_LoganRef_BPnd_reg.nii
When I visualize this file using tkmedit, the map looks fine (and is not cut
off).
However, after transforming this file into fsaverage space, it becomes cut off.
First I copied each individual volume file into each subject's mri folder. Then
I used this command to transform the individual files into mni305 space:
mri_vol2vol --mov fs_NNC112_0045_RBV_MC_s10v3_LoganRef_BPnd_reg.nii --targ
$FREESURFER_HOME/average/mni305.cor.subfov2.mgz --xfm transforms/talairach.xfm
--o fs_NNC112_0045_RBV_MC_s10v3_LoganRef_BPnd_reg_mni305.subfov2.mgz
Do you know why some of the volume maps are being cut off after transforming
them into fsaverage space?
Thanks for your help,
Anais
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[Freesurfer] QA measures
Dear Freesurfer Team, We would like to have a Q/A measure (or two) that would give us indication of how well your software worked on each of our data sets. Obviously some image sets will be noisier than others for a variety of reasons. Could you point us towards what options we may have for extracting such a measure from your processing pipeline? We were playing around with QAtools but wanted to understand if there is a systematic computation of say a handful of variables that would give us a global representation of how well things worked for each case we run? Something that we could compare across our patients and even across data sets? Best, KZ ___ 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.
