Re: [Freesurfer] qdec error message
Hi Nick I run Qdec 1.2 and all cases have been processed with freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0 Olivier On 25/05/2011, at 21:18, Nick Schmansky wrote: > what version of freesurfer does this happen with? > > n. > On Wed, 2011-05-25 at 14:17 +1000, Olivier Piguet wrote: >> Good afternoon, >> >> When running qdec, I receive the following error message: >> >> Writing to >> /Volumes/workingdata/FTD/T1/subjects/qdec/Untitled/contrasts.sig.mgh >> reading group avg surface area 822 cm^2 from file >> ERROR: could not find volume >> /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig. Does it >> exist? >> Reading in average area >> /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/lh.white.avg.area.mgh >> reading group avg surface area 1041 cm^2 from file >> ERROR: could not find volume >> /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig. Does it >> exist? >> Reading in average area >> /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/lh.pial.avg.area.mgh >> reading group avg surface area 822 cm^2 from file >> ERROR: could not find volume >> /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig. Does it >> exist? >> >> I have run all subjects with qcache and I am using fsaverage. I have checked >> the files in the fsaverage folder. Although the file orig. does not exist, >> there is a file called orig.mgz in the mri folder. I have tried to rename >> this file (i.e., removing the 'mgz' part) but this did not remove the error. >> >> Any suggestion would be appreciated. >> >> Thanks >> >> Olivier Piguet >> Neuroscience Research Australia >> Sydney NSW, Australia >> >> >> >> >> >> >> >> ___ >> 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
[Freesurfer] qdec error message
Good afternoon, When running qdec, I receive the following error message: Writing to /Volumes/workingdata/FTD/T1/subjects/qdec/Untitled/contrasts.sig.mgh reading group avg surface area 822 cm^2 from file ERROR: could not find volume /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig. Does it exist? Reading in average area /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/lh.white.avg.area.mgh reading group avg surface area 1041 cm^2 from file ERROR: could not find volume /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig. Does it exist? Reading in average area /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/lh.pial.avg.area.mgh reading group avg surface area 822 cm^2 from file ERROR: could not find volume /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig. Does it exist? I have run all subjects with qcache and I am using fsaverage. I have checked the files in the fsaverage folder. Although the file orig. does not exist, there is a file called orig.mgz in the mri folder. I have tried to rename this file (i.e., removing the 'mgz' part) but this did not remove the error. Any suggestion would be appreciated. Thanks Olivier Piguet Neuroscience Research Australia Sydney NSW, Australia ___ 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] pial edit on atrophied temporal pole
Thanks for the info. In severe cases of semantic dementia, you will see overall atrophy where the anterior temporal pole becomes almost non existent (combination of neuronal loss and white matter loss), probably also contributing to reduced white/grey differentiation. Is there a way to manually trace the pial surface on these slices or not? Because I have a large group of patients with semantic dementia that I would like to process, I am likely to encounter this problem again in the future. Thanks again for any suggestions and comments Olivier On 16/05/2009, at 0:20, Bruce Fischl wrote: thanks Mike. Was it the same situation, where there is no nearby white matter? I guess I don't really understand the anatomy. Is there really a place where you have 10mm of gray matter with no underlying white matter? Or is it unmeylinated white matter that we just can't see? On Fri, 15 May 2009, Michael Harms wrote: As an aside, in a Alzheimer/ elderly cohort of ~250, we had 12 subjects that we had to exclude for what sounds like a very similar reason -- we just couldn't get the pial surface in the anterior temporal lobe to properly encapsulate the gray matter. -Mike H. On Fri, 2009-05-15 at 12:24 +1000, Olivier Piguet wrote: That is correct. This is case of semantic dementia where left anterior temporal region is markedly atrophic. Olivier On 15/05/2009, at 9:15, Bruce Fischl wrote: so there's 10mm or so of gray matter with no underlying wm? I didn't think that was ever the case. What pathology is this in? And you're sure it's cortex, not amygdala? Jean: any thoughts? On Fri, 15 May 2009, Olivier Piguet wrote: Hi Bruce, In the coronal plane, slice 152 is the last slice where white matter is clearly visible. Then, slices 153-158, only grey matter is recognised but not all of it, and slices 159-164, grey matter is not recognised at all. I added control points on slice 151-153 in the hope that it would help but no luck. Olivier On 15/05/2009, at 8:39, Bruce Fischl wrote: Hi Oliver, how far away is the nearest white matter? Bruce On Fri, 15 May 2009, Olivier Piguet wrote: Hi there, I haven't received a reply to my question below. Just to clarify, I ran autorecon1 and autorecon2 on this subject. When examining the surfaces in tkmedit, the left temporal pole is not included in the pial surface. Is there a way to force freesurfer to recognise this as valid brain tissue, bearing in mind that there is no visible white matter underneath (and therefore the option of adding control points is not possible). Thanks for any suggestion to resolve this problem. Olivier On 13/05/2009, at 12:57, Olivier Piguet wrote: Hi there, I've run autorecon2 on a subject who has significant unilateral atrophy in the anterior temporal region. In the last few slices anteriorly, the pial surface does not include what is clearly atrophied cortical tissue without underlying white matter. What is the method to correct for this? Looking at previous queries, all of them refer to spots where one can manipulate the segmentation by adding control points in the neighbouring white matter, which is not present in this instance. Any suggestion appreciated. Olivier ~ Olivier Piguet Ph.D. NHMRC Fellow (Clinical Career Development Award) Conjoint Senior Lecturer UNSW Prince of Wales Medical Research Institute Barker St Randwick NSW 2031 Australia Voice: +61 2 9399 1113 Fax: +61 2 9399 1047 E-mail: o.pig...@powmri.edu.au http://www.ftdrg.org/ ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] pial edit on atrophied temporal pole
That is correct. This is case of semantic dementia where left anterior temporal region is markedly atrophic. Olivier On 15/05/2009, at 9:15, Bruce Fischl wrote: so there's 10mm or so of gray matter with no underlying wm? I didn't think that was ever the case. What pathology is this in? And you're sure it's cortex, not amygdala? Jean: any thoughts? On Fri, 15 May 2009, Olivier Piguet wrote: Hi Bruce, In the coronal plane, slice 152 is the last slice where white matter is clearly visible. Then, slices 153-158, only grey matter is recognised but not all of it, and slices 159-164, grey matter is not recognised at all. I added control points on slice 151-153 in the hope that it would help but no luck. Olivier On 15/05/2009, at 8:39, Bruce Fischl wrote: Hi Oliver, how far away is the nearest white matter? Bruce On Fri, 15 May 2009, Olivier Piguet wrote: Hi there, I haven't received a reply to my question below. Just to clarify, I ran autorecon1 and autorecon2 on this subject. When examining the surfaces in tkmedit, the left temporal pole is not included in the pial surface. Is there a way to force freesurfer to recognise this as valid brain tissue, bearing in mind that there is no visible white matter underneath (and therefore the option of adding control points is not possible). Thanks for any suggestion to resolve this problem. Olivier On 13/05/2009, at 12:57, Olivier Piguet wrote: Hi there, I've run autorecon2 on a subject who has significant unilateral atrophy in the anterior temporal region. In the last few slices anteriorly, the pial surface does not include what is clearly atrophied cortical tissue without underlying white matter. What is the method to correct for this? Looking at previous queries, all of them refer to spots where one can manipulate the segmentation by adding control points in the neighbouring white matter, which is not present in this instance. Any suggestion appreciated. Olivier ~~~~~ Olivier Piguet Ph.D. NHMRC Fellow (Clinical Career Development Award) Conjoint Senior Lecturer UNSW Prince of Wales Medical Research Institute Barker St Randwick NSW 2031 Australia Voice: +61 2 9399 1113 Fax: +61 2 9399 1047 E-mail: o.pig...@powmri.edu.au http://www.ftdrg.org/ ___ 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
Re: [Freesurfer] pial edit on atrophied temporal pole
Hi Bruce, In the coronal plane, slice 152 is the last slice where white matter is clearly visible. Then, slices 153-158, only grey matter is recognised but not all of it, and slices 159-164, grey matter is not recognised at all. I added control points on slice 151-153 in the hope that it would help but no luck. Olivier On 15/05/2009, at 8:39, Bruce Fischl wrote: Hi Oliver, how far away is the nearest white matter? Bruce On Fri, 15 May 2009, Olivier Piguet wrote: Hi there, I haven't received a reply to my question below. Just to clarify, I ran autorecon1 and autorecon2 on this subject. When examining the surfaces in tkmedit, the left temporal pole is not included in the pial surface. Is there a way to force freesurfer to recognise this as valid brain tissue, bearing in mind that there is no visible white matter underneath (and therefore the option of adding control points is not possible). Thanks for any suggestion to resolve this problem. Olivier On 13/05/2009, at 12:57, Olivier Piguet wrote: Hi there, I've run autorecon2 on a subject who has significant unilateral atrophy in the anterior temporal region. In the last few slices anteriorly, the pial surface does not include what is clearly atrophied cortical tissue without underlying white matter. What is the method to correct for this? Looking at previous queries, all of them refer to spots where one can manipulate the segmentation by adding control points in the neighbouring white matter, which is not present in this instance. Any suggestion appreciated. Olivier ~~~~~ Olivier Piguet Ph.D. NHMRC Fellow (Clinical Career Development Award) Conjoint Senior Lecturer UNSW Prince of Wales Medical Research Institute Barker St Randwick NSW 2031 Australia Voice: +61 2 9399 1113 Fax: +61 2 9399 1047 E-mail: o.pig...@powmri.edu.au http://www.ftdrg.org/ ___ 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
[Freesurfer] pial edit on atrophied temporal pole
Hi there, I haven't received a reply to my question below. Just to clarify, I ran autorecon1 and autorecon2 on this subject. When examining the surfaces in tkmedit, the left temporal pole is not included in the pial surface. Is there a way to force freesurfer to recognise this as valid brain tissue, bearing in mind that there is no visible white matter underneath (and therefore the option of adding control points is not possible). Thanks for any suggestion to resolve this problem. Olivier On 13/05/2009, at 12:57, Olivier Piguet wrote: Hi there, I've run autorecon2 on a subject who has significant unilateral atrophy in the anterior temporal region. In the last few slices anteriorly, the pial surface does not include what is clearly atrophied cortical tissue without underlying white matter. What is the method to correct for this? Looking at previous queries, all of them refer to spots where one can manipulate the segmentation by adding control points in the neighbouring white matter, which is not present in this instance. Any suggestion appreciated. Olivier ~~~~~ Olivier Piguet Ph.D. NHMRC Fellow (Clinical Career Development Award) Conjoint Senior Lecturer UNSW Prince of Wales Medical Research Institute Barker St Randwick NSW 2031 Australia Voice: +61 2 9399 1113 Fax: +61 2 9399 1047 E-mail: o.pig...@powmri.edu.au http://www.ftdrg.org/ ___ 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
[Freesurfer] pial edit on atrophied temporal pole
Hi there, I've run autorecon2 on a subject who has significant unilateral atrophy in the anterior temporal region. In the last few slices anteriorly, the pial surface does not include what is clearly atrophied cortical tissue without underlying white matter. What is the method to correct for this? Looking at previous queries, all of them refer to spots where one can manipulate the segmentation by adding control points in the neighbouring white matter, which is not present in this instance. Any suggestion appreciated. Olivier ~ Olivier Piguet Ph.D. NHMRC Fellow (Clinical Career Development Award) Conjoint Senior Lecturer UNSW Prince of Wales Medical Research Institute Barker St Randwick NSW 2031 Australia Voice: +61 2 9399 1113 Fax: +61 2 9399 1047 E-mail: o.pig...@powmri.edu.au http://www.ftdrg.org/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] unable to run mc-sess with bert dataset
Title: Olivier Piguet, Ph Good morning, I recently installed the new version of FreeSurfer and have been re-familiarising myself with the steps/procedures. I followed the FreeSurfer and FsFast tutorial which went fine until I tried the step described in the FsFastTutorial/700: Motion correct the data. When I ran the command: mc-sess -sf sessid -df sesspar I received the following error message: Logfile is /home/olivierp/BERT_TUTORIAL_ANALYSES/log/mc-bert-functional-bold.log --- /home/olivierp/FreeSurfer_tutorial/bert-functional RunList: 007 008 009 Targ Stem is 007/f --- ** --- --- Motion Correcting Run 007 --- --- ** --- sess = bert-functional Fri May 26 08:27:34 EST 2006 mc-afni -i 007/f -o 007/fmc -t 007/f -toff 0 -ipr 3.1250 -bpr 6. 0007484366104649 -TR 2 ERROR: cannot find AFNI command to3d Any help/suggestion on how to solve this problem would be greatly appreciated. Olivier Piguet -- Olivier Piguet, Ph.D. Prince of Wales Medical Research Institute Barker St Randwick NSW 2031 Australia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] selxavg-sess: error message
I tried the gammafit option but I am getting the same error message whether I specify a time window or not. Is there anything else that I should check? The parafile contains 19 conditions + null. It is based on the subjects' responses (6 possible responses for 3 stimulus types = 18 conditions; 1 missing response condition). The TR is 2 s. Stimuli are presented every 4 s (2 s for fixation points). We have three retrieval runs. Each contains 146 items (37 stimuli x 3 categories and 35 fixations). Thanks Olivier At 11:28 AM -0400 7/21/04, Doug Greve wrote: This means that the design matrix is ill-conditioned. This can happen if your using an FIR model (ie, not using -gammafit) and the stimuli are presented with some fixed timing with respect to each other with the elapsed time between them being less than the FIR time window. For example, if you presented a stimulus every 16 sec but had a 20 sec time window. Or if one stimulus is always followed by another with a fixed delay. I suspect the latter is the case as it's hard to avoid with a memory task. Unfortunately, you're pretty much forced to assume a shape to the hemodynamic response (ie, use gammafit). doug Olivier Piguet wrote: Good morning, I am getting the following error message whilst trying to run the selxavg-sess command: ERROR: paradigm is ill-conditioned (5.37345e+18). Check your paradigm file for file for periodicities or for some event types that all ways follow other event types (or itself). >> >> quiting matlab -- ERROR: fast_selxavg() failed ERROR (/autofs/space/engram_010/users/rk_fmri_test/YNS15_060404): selxavg failed What is the meaning of this message? I have checked the mail archives but couldn't find any information. I am analysing data for a retrieval memory task and the para file (number of conditions and response types) is based on the subject responses and therefore some response types may or may not be repeating themselves. Thanks Olivier -- --------- Olivier Piguet, Ph.D. Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE 20-392 77 Massachusetts Avenue Cambridge MA 02139 USA For overnight or express deliveries, send to: 3 Cambridge Center Suite 392 Cambridge, MA 02142 USA Voice: (+ 1) 617-253-8976 Fax: (+ 1) 617-253-1504 E-mail: [EMAIL PROTECTED] ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 -- --------- Olivier Piguet, Ph.D. Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE 20-392 77 Massachusetts Avenue Cambridge MA 02139 USA For overnight or express deliveries, send to: 3 Cambridge Center Suite 392 Cambridge, MA 02142 USA Voice: (+ 1) 617-253-8976 Fax: (+ 1) 617-253-1504 E-mail: [EMAIL PROTECTED] ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] selxavg-sess: error message
Good morning, I am getting the following error message whilst trying to run the selxavg-sess command: ERROR: paradigm is ill-conditioned (5.37345e+18). Check your paradigm file for file for periodicities or for some event types that all ways follow other event types (or itself). >> quiting matlab -- ERROR: fast_selxavg() failed ERROR (/autofs/space/engram_010/users/rk_fmri_test/YNS15_060404): selxavg failed What is the meaning of this message? I have checked the mail archives but couldn't find any information. I am analysing data for a retrieval memory task and the para file (number of conditions and response types) is based on the subject responses and therefore some response types may or may not be repeating themselves. Thanks Olivier -- --------- Olivier Piguet, Ph.D. Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE 20-392 77 Massachusetts Avenue Cambridge MA 02139 USA For overnight or express deliveries, send to: 3 Cambridge Center Suite 392 Cambridge, MA 02142 USA Voice: (+ 1) 617-253-8976 Fax: (+ 1) 617-253-1504 E-mail: [EMAIL PROTECTED] ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
