[Freesurfer] Postdoctoral Position in Division of Neurotherapeutics at MGH/HMS (Boston, MA)
Hi everyone, The Division of Neurotherapeutics at Massachusetts General Hospital (Boston, MA) has an open postdoctoral position. The posting is below: NEUROIMAGING POSTDOCTORAL POSITION IN DIVISION OF NEUROTHERAPEUTICS AT HARVARD MEDICAL SCHOOL/ MASSACHUSETTS GENERAL HOSPITAL The Division of Neurotherapeutics at the Massachusetts General Hospital is looking for a neuroimaging postdoctoral fellow to join the research group of Drs. Darin Dougherty MD, Thilo Deckersbach PhD and Alik Widge MD PhD. Overview Research projects will focus on developing pipelines for multi-modal MRI analysis with the aim of investigating psychopathology along transdiagnstic domains under the TRANSFORM DBS project, using task-based and resting-state fMRI and structural MRI data. The post-doctoral fellow will have the opportunity to collaborate and work with an interdisciplinary team of clinicians, neuroscientists and engineers and have significant opportunities to advance their career. Your Profile We seek a postdoctoral candidate with a Ph.D. in psychology, neuroscience, or related discipline with an interest translational neuroscience with a strong background in Python, Matlab, or R. The ideal candidate would have extensive knowledge of computational neuroimaging. Expertise in cognitive modeling, graph theory, or machine learning is also highly desirable. Knowledge of common neuroimaging software, especially FreeSurfer and FSL, is also appreciated. Interest in understanding mechanisms underlying major psychiatric disorders and enthusiasm for working with psychiatric populations is necessary. Highly motivated individuals with a record of productive research are encouraged to apply. Benefits Benefits of this postdoctoral position include (1) access to numerous sets of high-quality, multi-modal MRI data; (2) opportunities to analyze and publish on these datasets; (3) mentoring for career development; and (4) access to imaging experts from around the world and to state-of-the-art tools for the development of neuroscientific and clinical research at the Martinos Center. Lab Description The Division of Neurotherapeutics at MGH is a multidisciplinary translational neuroscience group located at the Athinoula A. Martinos Center for Biomedical Imaging in Charlestown, MA. Our focus is on neurotherapeutic interventions for severe, treatment-resistant psychiatric illnesses, particularly for major depressive disorder, obsessive compulsive disorder, anxiety disorders, and eating disorders. Our research spans both mechanistic studies, clinical trials, and device-based interventions employing a variety of techniques, including neuroimaging and electrophysiology. We also provide clinical services and surgical treatments for psychiatric illness. Our work utilizes functional and structural magnetic resonance imaging (fMRI), positron emission tomography (PET), electroencephalography (EEG), magnetoencephalography (MEG) to further understanding of psychiatric illness and treatment. We use transcranial magnetic stimulation (TMS), vagus nerve stimulation (VNS) and deep brain stimulation (DBS) as tools to both treat disease and understand the neural correlates of mental illness. Lab Website: http://www.massgeneral.org/psychiatry/research/researchlab.aspx?id=1659 Contact: Afsana Afzal - aaf...@mgh.harvard.edu __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ___ 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] Bad Coregistration - Left-Right Reversed
I opened up the functional and anatomical (original and reversed) in freeview and the functional volume is better aligned with the reversed anatomical than with the original anatomical. I realize this is a gross visual check that is probably unreliable but I don't have any other guesses as so why the coreg is failing for over 150 subjects. __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, August 17, 2016 1:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed what do you mean "visual inspection shows that they are actually reversed"? Please give details On 08/17/2016 01:31 PM, Afzal, Afsana wrote: > I'm trying to understand why the coregistration for a bunch of subjects are > bad/failing (mincost value > 8). > > The orientation for the anatomical matches the functional (after FSL > unpacking) but visual inspection shows that they are actually reversed. Then > I used mri_convert to change the orientation of the anatomical but the > coregistration is still failing. So I still have no idea what's causing the > coreg to fail or how to fix it. > > -Afsana > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Tuesday, August 16, 2016 5:51 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed > > I'm still not sure why you are trying to do this. If FSL did not unpack > the volumes with the correct orientation, then you need to switch to > mri_convert. If they are in the right orientation, then I don't > understand what you are trying to do. > doug > > On 08/16/2016 05:27 PM, Afzal, Afsana wrote: >> Hi Doug, >> >> After the coregistration failed for the majority of the subjects, I visually >> inspected a handful of the subjects in freeview and it looks like the >> anatomical and the functional are reversed but I could be wrong. >> >> The nifti files are unpacked from DICOMs using unpack_fsl.sh >> (/cluster/nrg/tools/0.10.0/code/lib/shell/unpack_fsl.sh). I can point you to >> a specific subject directory if that would be of any help. >> >> Might be worth mentioning that the subjects who failed coreg were not >> scanned using siemens scanners but Phillips and GE scanners. Don't know if >> there's some sort of discrepancy between the scanner coordinate frames that >> could potentially lead to this issue. >> >> Thank you very much for your help, >> >> Afsana >> __ >> Afsana Afzal >> Clinical Research Coordinator >> Massachusetts General Hospital >> Division of Neurotherapeutics >> Department of Psychiatry: Neurosciences >> 149 13th St, Room 2612 >> Charlestown, MA 02129 >> Phone: 617-643-5129 >> Fax: 617-726-4078 >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: Tuesday, August 16, 2016 3:45 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed >> >> How do you know that the structural is left-right reversed? Or that the >> fMRI is? How did you create the nifti files? >> >> >> On 08/16/2016 01:41 PM, Afzal, Afsana wrote: >>> Hi, >>> >>> I'm having trouble co-registering a bunch of subjects whose T1 is >>> left-right reversed. While the orientation of the structural file in >>> the NIfTI header is LIA and the orientation of the functional volume >>> is LAS, visual inspection shows that the structural is left-right >>> reversed. I then followed the steps outlined in >>> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal >>> <https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal> to rerun >>> the reconstruction and re-registered the subject but the registration >>> mincost value is still hovering around 0.9 even with the left-right >>> reversed structural. >>> >>> I've tried running registration with SPM and FSL; neither
Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
I'm trying to understand why the coregistration for a bunch of subjects are bad/failing (mincost value > 8). The orientation for the anatomical matches the functional (after FSL unpacking) but visual inspection shows that they are actually reversed. Then I used mri_convert to change the orientation of the anatomical but the coregistration is still failing. So I still have no idea what's causing the coreg to fail or how to fix it. -Afsana From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, August 16, 2016 5:51 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed I'm still not sure why you are trying to do this. If FSL did not unpack the volumes with the correct orientation, then you need to switch to mri_convert. If they are in the right orientation, then I don't understand what you are trying to do. doug On 08/16/2016 05:27 PM, Afzal, Afsana wrote: > Hi Doug, > > After the coregistration failed for the majority of the subjects, I visually > inspected a handful of the subjects in freeview and it looks like the > anatomical and the functional are reversed but I could be wrong. > > The nifti files are unpacked from DICOMs using unpack_fsl.sh > (/cluster/nrg/tools/0.10.0/code/lib/shell/unpack_fsl.sh). I can point you to > a specific subject directory if that would be of any help. > > Might be worth mentioning that the subjects who failed coreg were not scanned > using siemens scanners but Phillips and GE scanners. Don't know if there's > some sort of discrepancy between the scanner coordinate frames that could > potentially lead to this issue. > > Thank you very much for your help, > > Afsana > __ > Afsana Afzal > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Tuesday, August 16, 2016 3:45 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed > > How do you know that the structural is left-right reversed? Or that the > fMRI is? How did you create the nifti files? > > > On 08/16/2016 01:41 PM, Afzal, Afsana wrote: >> Hi, >> >> I'm having trouble co-registering a bunch of subjects whose T1 is >> left-right reversed. While the orientation of the structural file in >> the NIfTI header is LIA and the orientation of the functional volume >> is LAS, visual inspection shows that the structural is left-right >> reversed. I then followed the steps outlined in >> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal >> <https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal> to rerun >> the reconstruction and re-registered the subject but the registration >> mincost value is still hovering around 0.9 even with the left-right >> reversed structural. >> >> I've tried running registration with SPM and FSL; neither method is >> able to register these subjects properly. >> >> With --init-fsl I get the following: >> WARNING: initial G-W contrast is negative, but expecting positive. >> If the mov data has a T1 contrast, re-run with --T1 >> >> and with --init-spm I get: >> WARNING: bad orientation matrix (determinant = 0) in nifti1 file ... >> ... continuing. >> >> At this point I'm out of ideas to try out. This issue is occurring for >> over 170 subjects (data collected outside Martinos using non-siemens >> scanners). >> >> Any help would be much appreciated! >> >> Thanks, >> >> Afsana >> >> >> >> __ >> *Afsana Afzal* >> Clinical Research Coordinator >> Massachusetts General Hospital >> Division of Neurotherapeutics >> Department of Psychiatry: Neurosciences >> 149 13th St, Room 2612 >> Charlestown, MA 02129 >> Phone: 617-643-5129 >> Fax: 617-726-4078 >> >> >> ___ >> 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 >
Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
Hi Doug, After the coregistration failed for the majority of the subjects, I visually inspected a handful of the subjects in freeview and it looks like the anatomical and the functional are reversed but I could be wrong. The nifti files are unpacked from DICOMs using unpack_fsl.sh (/cluster/nrg/tools/0.10.0/code/lib/shell/unpack_fsl.sh). I can point you to a specific subject directory if that would be of any help. Might be worth mentioning that the subjects who failed coreg were not scanned using siemens scanners but Phillips and GE scanners. Don't know if there's some sort of discrepancy between the scanner coordinate frames that could potentially lead to this issue. Thank you very much for your help, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, August 16, 2016 3:45 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed How do you know that the structural is left-right reversed? Or that the fMRI is? How did you create the nifti files? On 08/16/2016 01:41 PM, Afzal, Afsana wrote: > Hi, > > I'm having trouble co-registering a bunch of subjects whose T1 is > left-right reversed. While the orientation of the structural file in > the NIfTI header is LIA and the orientation of the functional volume > is LAS, visual inspection shows that the structural is left-right > reversed. I then followed the steps outlined in > https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal > <https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal> to rerun > the reconstruction and re-registered the subject but the registration > mincost value is still hovering around 0.9 even with the left-right > reversed structural. > > I've tried running registration with SPM and FSL; neither method is > able to register these subjects properly. > > With --init-fsl I get the following: > WARNING: initial G-W contrast is negative, but expecting positive. > If the mov data has a T1 contrast, re-run with --T1 > > and with --init-spm I get: > WARNING: bad orientation matrix (determinant = 0) in nifti1 file ... > ... continuing. > > At this point I'm out of ideas to try out. This issue is occurring for > over 170 subjects (data collected outside Martinos using non-siemens > scanners). > > Any help would be much appreciated! > > Thanks, > > Afsana > > > > __ > *Afsana Afzal* > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > ___ > 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 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] Bad Coregistration - Left-Right Reversed
Hi, I'm having trouble co-registering a bunch of subjects whose T1 is left-right reversed. While the orientation of the structural file in the NIfTI header is LIA and the orientation of the functional volume is LAS, visual inspection shows that the structural is left-right reversed. I then followed the steps outlined in https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal to rerun the reconstruction and re-registered the subject but the registration mincost value is still hovering around 0.9 even with the left-right reversed structural. I've tried running registration with SPM and FSL; neither method is able to register these subjects properly. With --init-fsl I get the following: WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 and with --init-spm I get: WARNING: bad orientation matrix (determinant = 0) in nifti1 file ... ... continuing. At this point I'm out of ideas to try out. This issue is occurring for over 170 subjects (data collected outside Martinos using non-siemens scanners). Any help would be much appreciated! Thanks, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ___ 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] Beta-Zero Correction - No Phase File
Hi Doug, Thanks for getting back to me. I've tried mri_convert $Input_file --split $Output_file to split up the fieldmaps but I'm getting 6 to 12 different outputs (depending on the fieldmap) rather than just the mag and phase files which is what I was expecting. Have you encountered this before and is there another way to unpack the fieldmaps into just the mag and phase components? Thanks so much for you time, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2016 12:51 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Beta-Zero Correction - No Phase File You can extract frames from a multi frame file with mri_convert input.nii.gz --frame 0 output.frame0.nii.gz On 07/12/2016 02:29 PM, Afzal, Afsana wrote: > Hi, > > I'm working with a dataset that outputs only one file (not two > separate mag and phase files) for the fieldmap. The data was also > collected on non-Siemens scanners: Philips Ingenia and GE SIGNA HDx > (not sure if this is the reason the fieldmaps are unpacking > differently). I've attached the .dat file for one of the fieldmaps in > this email. > > If there a way to separate out the mag and phase from the single > fieldmap file so I can use epidewarp.fsl? > > Thanks, > > Afsana > > __ > *Afsana Afzal* > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > ___ > 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 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] Beta-Zero Correction - No Phase File
Hi, Just wanted to follow up on the issue of just having one fieldmap file for beta-zero correction outlined below. Thanks for your help, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana [aaf...@mgh.harvard.edu] Sent: Tuesday, July 12, 2016 2:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Beta-Zero Correction - No Phase File Hi, I'm working with a dataset that outputs only one file (not two separate mag and phase files) for the fieldmap. The data was also collected on non-Siemens scanners: Philips Ingenia and GE SIGNA HDx (not sure if this is the reason the fieldmaps are unpacking differently). I've attached the .dat file for one of the fieldmaps in this email. If there a way to separate out the mag and phase from the single fieldmap file so I can use epidewarp.fsl? Thanks, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ___ 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] Beta-Zero Correction - No Phase File
Hi, I'm working with a dataset that outputs only one file (not two separate mag and phase files) for the fieldmap. The data was also collected on non-Siemens scanners: Philips Ingenia and GE SIGNA HDx (not sure if this is the reason the fieldmaps are unpacking differently). I've attached the .dat file for one of the fieldmaps in this email. If there a way to separate out the mag and phase from the single fieldmap file so I can use epidewarp.fsl? Thanks, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 b0map-infodump.dat Description: b0map-infodump.dat ___ 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] Creating spheres in the volume
Hi, This question might have already been answered before but is there a way to take a coordinate in MNI space and create, say, a 5mm sphere in the volume? My goal is to take the sphere in the volume and convert it to a label using something like mri_vol2surf. Thanks for your help, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ___ 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 doubling file size
Hi everyone, I'm using mri_convert to reinforce TR information into the Nifti header in the following manner: mri_convert $FILE $FILE -tr $TR Before the conversion, my file size is usually around 550MB but after the conversion is doubles in size to ~1.1GB. In the Nifto file header I've noticed that the data type usually changes from int16 to float32. Is there a quick way to decrease the file size or revert back to int16 without affecting the data? Thanks for you help, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ___ 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] Group level analysis: Specifying contrasts
The source data is from a gambling task that has multiple levels of risk and reward. The offset refers to the risk level and the slope refers to the monetary reward for that particular risk level. We were doing some parametric modulation in the first level analysis. For the second levels, currently I'm just looking at the offset values which is why the slope rows are all zeros. Please let me know if that makes sense, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, April 11, 2016 11:19 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group level analysis: Specifying contrasts What is your source data? It looks like you have two time points per subject, but the names of "offset" and "slope" suggest some preprocessing? Input hc001-lRsk_offset hc001100 Input hc001-lRsk_slope hc001000 Input hc001-mRsk_offset hc001010 Input hc001-mRsk_slope hc001000 Input hc001-hRsk_offset hc001001 Input hc001-hRsk_slope hc001000 On 04/11/2016 10:09 AM, Afzal, Afsana wrote: > Hi Doug, > > I've attached the fsgd file and the contrast matrix file. Thanks for your > help! > > - Afsana > > __ > Afsana Afzal > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Friday, April 08, 2016 12:07 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Group level analysis: Specifying contrasts > > I don't know what you mean, can you just send the header of the fsgd > file and the contrast matrix? > > On 04/04/2016 11:20 AM, Afzal, Afsana wrote: >> Hi, >> >> I want to perform a linear regression for a task with 3 different risk >> conditions (low, medium, high) with the following linear trend: low = >> 1, medium = 2, high = 3. >> >> Right now I'm specifying the above weighted under each risk condition >> in my contrast matrix. Is this the correct approach? I want to make >> sure I am calculating a regression and not a weighted average. >> >> Thank you for your help, >> >> Afsana >> >> >> __ >> *Afsana Afzal* >> Clinical Research Coordinator >> Massachusetts General Hospital >> Division of Neurotherapeutics >> Department of Psychiatry: Neurosciences >> 149 13th St, Room 2612 >> Charlestown, MA 02129 >> Phone: 617-643-5129 >> Fax: 617-726-4078 >> >> >> ___ >> 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 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 ___
Re: [Freesurfer] Group level analysis: Specifying contrasts
Hi Doug, I've attached the fsgd file and the contrast matrix file. Thanks for your help! - Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, April 08, 2016 12:07 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group level analysis: Specifying contrasts I don't know what you mean, can you just send the header of the fsgd file and the contrast matrix? On 04/04/2016 11:20 AM, Afzal, Afsana wrote: > Hi, > > I want to perform a linear regression for a task with 3 different risk > conditions (low, medium, high) with the following linear trend: low = > 1, medium = 2, high = 3. > > Right now I'm specifying the above weighted under each risk condition > in my contrast matrix. Is this the correct approach? I want to make > sure I am calculating a regression and not a weighted average. > > Thank you for your help, > > Afsana > > > __ > *Afsana Afzal* > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > ___ > 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 avg.risk.mod.fsgd Description: avg.risk.mod.fsgd weight_avg.mtx Description: weight_avg.mtx ___ 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] Group level analysis: Specifying contrasts
Hi, I want to perform a linear regression for a task with 3 different risk conditions (low, medium, high) with the following linear trend: low = 1, medium = 2, high = 3. Right now I'm specifying the above weighted under each risk condition in my contrast matrix. Is this the correct approach? I want to make sure I am calculating a regression and not a weighted average. Thank you for your help, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ___ 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] Mismatch in dimensions using mri_label2vol
That works perfectly, thank you! __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, April 01, 2016 11:59 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mismatch in dimensions using mri_label2vol Use mri_label2label specifying the source and target subjects to be the same, a regmethod as surface, and select the --outmask option On 04/01/2016 11:37 AM, Afzal, Afsana wrote: > Hi Doug, > > I'm trying to map a cortical label onto the surface (i.e. extract a nifti > file for a particular label). So instead of a label.label file, it's a > label.nii that I can load in as an overlay in, say, tksurfer. Is there a way > to do this using freesurfer commands? > > __ > Afsana Afzal > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Monday, March 28, 2016 11:16 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Mismatch in dimensions using mri_label2vol > > Sorry, what are you trying to do? mri_label2vol maps a label (ie, ROI, > segmentataion, annotation) into a volume space. Do you just want to map > the surface overlay (fmcpr.sm4.fsaverage.lh.b0dc.nii) into the volume > space? If so, use mri_surf2vol. You can use the version below (using > method1 from the help) > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol > > > On 03/28/2016 10:13 AM, Afzal, Afsana wrote: >> Hi, Just wanted to follow up on the issue below regarding the >> dimension of the mri_label2vol output. >> >> >> Hi, >> >> I'm using mri_label2vol with the parameters below but the output .nii >> volume has the shape 163842x1x1 while the input volume is27307x1x6. >> This dimension mismatch is causing issues in our gPPI pipeline. >> >> How can I generate a .nii output file with the27307x1x6 dimension? >> >> mri_label2vol >> --temp fmcpr.sm4.fsaverage.lh.b0dc.nii (output file generated from >> preproc step) >> --label label_name.label >> --o label_name.nii >> --identity >> >> Thanks, >> >> Afsana >> __ >> *Afsana Afzal* >> Clinical Research Coordinator >> Massachusetts General Hospital >> Division of Neurotherapeutics >> Department of Psychiatry: Neurosciences >> 149 13th St, Room 2612 >> Charlestown, MA 02129 >> Phone: 617-643-5129 >> Fax: 617-726-4078 >> >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana >> [aaf...@mgh.harvard.edu] >> *Sent:* Wednesday, March 23, 2016 2:44 PM >> *To:* freesurfer@nmr.mgh.harvard.edu >> *Subject:* [Freesurfer] Mismatch in dimensions using mri_label2vol >> >> Hi, >> >> I'm using mri_label2vol with the parameters below but the output .nii >> volume has the shape 163842x1x1 while the input volume is27307x1x6. >> This dimension mismatch is causing issues in our gPPI pipeline. >> >> How can I generate a .nii output file with the27307x1x6 dimension? >> >> mri_label2vol >> --temp fmcpr.sm4.fsaverage.lh.b0dc.nii (output file generated from >> preproc step) >> --label label_name.label >> --o label_name.nii >> --identity >> >> Thanks, >> >> Afsana >> >> __ >> *Afsana Afzal* >> Clinical Research Coordinator >> Massachusetts General Hospital >> Division of Neurotherapeutics >> Department of Psychiatry: Neurosciences >> 149 13th St, Room 2612 >> Charlestown, MA 02129 >> Phone: 617-643-5129 >> Fax: 617-726-4078 >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/li
Re: [Freesurfer] Mismatch in dimensions using mri_label2vol
Hi, Just wanted to follow up on the issue below regarding the dimension of the mri_label2vol output. Hi, I'm using mri_label2vol with the parameters below but the output .nii volume has the shape 163842x1x1 while the input volume is 27307x1x6. This dimension mismatch is causing issues in our gPPI pipeline. How can I generate a .nii output file with the 27307x1x6 dimension? mri_label2vol --temp fmcpr.sm4.fsaverage.lh.b0dc.nii (output file generated from preproc step) --label label_name.label --o label_name.nii --identity Thanks, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana [aaf...@mgh.harvard.edu] Sent: Wednesday, March 23, 2016 2:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Mismatch in dimensions using mri_label2vol Hi, I'm using mri_label2vol with the parameters below but the output .nii volume has the shape 163842x1x1 while the input volume is 27307x1x6. This dimension mismatch is causing issues in our gPPI pipeline. How can I generate a .nii output file with the 27307x1x6 dimension? mri_label2vol --temp fmcpr.sm4.fsaverage.lh.b0dc.nii (output file generated from preproc step) --label label_name.label --o label_name.nii --identity Thanks, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ___ 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] Mismatch in dimensions using mri_label2vol
Hi, I'm using mri_label2vol with the parameters below but the output .nii volume has the shape 163842x1x1 while the input volume is 27307x1x6. This dimension mismatch is causing issues in our gPPI pipeline. How can I generate a .nii output file with the 27307x1x6 dimension? mri_label2vol --temp fmcpr.sm4.fsaverage.lh.b0dc.nii (output file generated from preproc step) --label label_name.label --o label_name.nii --identity Thanks, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ___ 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] [FreeSurfer] Repeated Measures ANOVA in FSFAST
Hi Doug, Upon reviewing the repeated measures ANOVA tutorial on the Freesurfer website I was able to revise the fsgd file (below) to what I now think is more accurate. I'm treating each observation of a condition (risk-reward pairing) and indicating that each of those observations belong to the same subject (Subject1, Subject2, etc). GroupDescriptorFile 1 Class Subject1 Class Subject2 VariableshRisk-vs-lRisk hRisk-vs-mRisk Input Subject1-lRsk_lRwd Subject1 -1 0 Input Subject1-lRsk_mRwd Subject1 -1 0 Input Subject1-lRsk_hRwd Subject1 -1 0 Input Subject1-mRsk_lRwd Subject1 0 -1 Input Subject1-mRsk_mRwd Subject1 0 -1 Input Subject1-mRsk_hRwd Subject1 0 -1 Input Subject1-hRsk_lRwd Subject1 1 1 Input Subject1-hRsk_mRwd Subject1 1 1 Input Subject1-hRsk_hRwd Subject1 1 1 Input Subject2-lRsk_lRwd Subject1 -1 0 Input Subject2-lRsk_mRwd Subject1 -1 0 Input Subject2-lRsk_hRwd Subject1 -1 0 Input Subject2-mRsk_lRwd Subject1 0 -1 Input Subject2-mRsk_mRwd Subject1 0 -1 Input Subject2-mRsk_hRwd Subject1 0 -1 Input Subject2-hRsk_lRwd Subject1 1 1 Input Subject2-hRsk_mRwd Subject1 1 1 Input Subject2-hRsk_hRwd Subject1 1 1 Please let me know if you think this design looks more correct given the observations per subject. Thanks for your help, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana [aaf...@mgh.harvard.edu] Sent: Monday, February 22, 2016 2:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST Hi, Sorry about the lack of clarification. Yes, it's a functional study. Each of the classes is a subject. I basically want to compute the main effect of risk at the group level (i.e. High Risk minus Low Risk) but there are multiple observations per risk level since there are three different reward levels within each risk level (low Reward, med Reward, high Reward). I was thinking of setting up all the risk-reward conditions as active (=1s) in the fsgd file and then subtracting the conditions using the contrast matrices below to get the main effect of Risk. Please let me know if that makes a bit more sense. Thanks for your help, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, February 22, 2016 12:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST I'm having a hard time deciphering what you are doing. Is this a functional study? What are the 5 classes? Why are there all 1s regardless of risk or reward level? On 02/19/2016 10:52 AM, Afzal, Afsana wrote: > Hi, > > I'm analyzing a decision making task with a 3x3 condition matrix: > pairings of low, medium, high levels of risk with low, medium, high > levels of reward. > > I've set up the following FSGD file to do a repeated > measures/within-subject ANOVA: > > GroupDescriptorFile 1 > Class hc001 > Class hc002 > Class hc003 > Class hc004 > Class hc005 > Variables lRsk_lRwd lRsk_mRwd lRsk_hRwd mRsk_lRwd > mRsk_mRwd mRsk_hRwd hRsk_lRwd hRsk_mRwd hRsk_hRwd > Input hc001 hc001 1 1 1 1 1 1 > 1 1 1 > Input hc002 hc002 1 1 1 1 1 1 > 1 1 1 > Input hc003 hc003 1 1 1 1 1 1 > 1 1 1 > Input hc004 hc004 1 1 1 1 1 1 > 1 1 1 > Input hc005 hc005 1 1 1 1 1 1 > 1 1 1 > > I've also created the following contrast matrices: > > Con1: Does difference between highRisk andLowRisk differ from 0? > 0 0 0 0 0 -1 -1 -1 0 0 0 1 1 1 > > Con2: Does difference between highRisk andMedRisk differ from 0? > 0 0 0 0 0 0 0 0 -1 -1 -1 1 1 1 > > Is this an appropriate way of setting up the ANOVA? > > Thanks for your help, > > Afsana > __ > *Afsana Afzal* > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617
Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST
Hi, Sorry about the lack of clarification. Yes, it's a functional study. Each of the classes is a subject. I basically want to compute the main effect of risk at the group level (i.e. High Risk minus Low Risk) but there are multiple observations per risk level since there are three different reward levels within each risk level (low Reward, med Reward, high Reward). I was thinking of setting up all the risk-reward conditions as active (=1s) in the fsgd file and then subtracting the conditions using the contrast matrices below to get the main effect of Risk. Please let me know if that makes a bit more sense. Thanks for your help, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, February 22, 2016 12:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST I'm having a hard time deciphering what you are doing. Is this a functional study? What are the 5 classes? Why are there all 1s regardless of risk or reward level? On 02/19/2016 10:52 AM, Afzal, Afsana wrote: > Hi, > > I'm analyzing a decision making task with a 3x3 condition matrix: > pairings of low, medium, high levels of risk with low, medium, high > levels of reward. > > I've set up the following FSGD file to do a repeated > measures/within-subject ANOVA: > > GroupDescriptorFile 1 > Class hc001 > Class hc002 > Class hc003 > Class hc004 > Class hc005 > Variables lRsk_lRwd lRsk_mRwd lRsk_hRwd mRsk_lRwd > mRsk_mRwd mRsk_hRwd hRsk_lRwd hRsk_mRwd hRsk_hRwd > Input hc001 hc0011 1 1 1 1 1 > 1 1 1 > Input hc002 hc002 1 1 1 1 1 1 > 1 1 1 > Input hc003 hc003 1 1 1 1 1 1 > 1 1 1 > Input hc004 hc004 1 1 1 1 1 1 > 1 1 1 > Input hc005 hc005 1 1 1 1 1 1 > 1 1 1 > > I've also created the following contrast matrices: > > Con1: Does difference between highRisk andLowRisk differ from 0? > 0 0 0 0 0 -1 -1 -1 0 0 0 1 1 1 > > Con2: Does difference between highRisk andMedRisk differ from 0? > 0 0 0 0 0 0 0 0 -1 -1 -1 1 1 1 > > Is this an appropriate way of setting up the ANOVA? > > Thanks for your help, > > Afsana > __ > *Afsana Afzal* > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > ___ > 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 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] [FreeSurfer] Repeated Measures ANOVA in FSFAST
Hi, Just wanted to check and see if the following is an appropriate set-up for a repeated measures ANOVA. Thanks, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana [aaf...@mgh.harvard.edu] Sent: Friday, February 19, 2016 10:52 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST Hi, I'm analyzing a decision making task with a 3x3 condition matrix: pairings of low, medium, high levels of risk with low, medium, high levels of reward. I've set up the following FSGD file to do a repeated measures/within-subject ANOVA: GroupDescriptorFile 1 Class hc001 Class hc002 Class hc003 Class hc004 Class hc005 Variables lRsk_lRwd lRsk_mRwd lRsk_hRwd mRsk_lRwd mRsk_mRwd mRsk_hRwd hRsk_lRwd hRsk_mRwd hRsk_hRwd Input hc001 hc0011 1 1 1 1 1 1 1 1 Input hc002 hc0021 1 1 1 1 1 1 1 1 Input hc003 hc0031 1 1 1 1 1 1 1 1 Input hc004 hc0041 1 1 1 1 1 1 1 1 Input hc005 hc0051 1 1 1 1 1 1 1 1 I've also created the following contrast matrices: Con1: Does difference between highRisk and LowRisk differ from 0? 0 0 0 0 0 -1 -1 -1 0 0 0 1 1 1 Con2: Does difference between highRisk and MedRisk differ from 0? 0 0 0 0 0 0 0 0-1 -1 -1 1 1 1 Is this an appropriate way of setting up the ANOVA? Thanks for your help, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ___ 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] [FreeSurfer] Repeated Measures ANOVA in FSFAST
Hi, I'm analyzing a decision making task with a 3x3 condition matrix: pairings of low, medium, high levels of risk with low, medium, high levels of reward. I've set up the following FSGD file to do a repeated measures/within-subject ANOVA: GroupDescriptorFile 1 Class hc001 Class hc002 Class hc003 Class hc004 Class hc005 Variables lRsk_lRwd lRsk_mRwd lRsk_hRwd mRsk_lRwd mRsk_mRwd mRsk_hRwd hRsk_lRwd hRsk_mRwd hRsk_hRwd Input hc001 hc0011 1 1 1 1 1 1 1 1 Input hc002 hc0021 1 1 1 1 1 1 1 1 Input hc003 hc0031 1 1 1 1 1 1 1 1 Input hc004 hc0041 1 1 1 1 1 1 1 1 Input hc005 hc0051 1 1 1 1 1 1 1 1 I've also created the following contrast matrices: Con1: Does difference between highRisk and LowRisk differ from 0? 0 0 0 0 0 -1 -1 -1 0 0 0 1 1 1 Con2: Does difference between highRisk and MedRisk differ from 0? 0 0 0 0 0 0 0 0-1 -1 -1 1 1 1 Is this an appropriate way of setting up the ANOVA? Thanks for your help, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ___ 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] How to convert a surface label to .nii
Hi, How can I convert a surface .label file to a .nii format? I'm using mri_label2label in the following way but the output is always in .label not .nii: mri_label2label --srclabel dlpfc-lh.label --outmask dlpfc-lh_mask.nii --s fsaverage --trglabel dlpfc-lh_mask.nii --regmethod surface --hemi lh Thanks for your help, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ___ 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] Interpreting white matter regressor dat file
Hi Doug, These are the first few lines of the wm.dat.pca-stats.dat file: 1 143481216.00 143481216.00 4.064.06 2 77359288.00 220840504.00 2.196.25 3 42542944.00 263383448.00 1.207.46 4 26329902.00 289713350.00 0.758.20 5 21830372.00 311543722.00 0.628.82 6 19145688.00 330689410.00 0.549.36 7 18512178.00 349201588.00 0.529.89 According to the functional connectivity tutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough), usually only the first 5 components are used for white matter regression. However, if I understand correctly, it looks like the first five components only remove ~8.82% cumulative variance, is that correct? If so, how should I go about choosing components for white matter regression? Thanks, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, January 13, 2016 12:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Interpreting white matter regressor dat file here you go (1) component number (2) variance spanned by that component (3) cumulative variance spanned up to that component (4) percent variance spanned by that component (5) cumulative percent variance spanned up to that component On 01/13/2016 09:56 AM, Afzal, Afsana wrote: > Hi, > > I have generated white matter regressor files for resting state > analysis using fcseed-config and fcseed-sess. The resulting files > include: wm.dat, wm.dat.pca-stats.dat and wm.dat.log. > > How do I interpret the wm.dat.pca-stats.dat file? There are 388 > numbered rows (I'm guessing one per acquisition since # of > acquisitions is 388?) and five columns. What do the columns represent? > > > Thanks for your help! > > - Afsana > > __ > *Afsana Afzal* > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > ___ > 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 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] Interpreting white matter regressor dat file
Hi, I have generated white matter regressor files for resting state analysis using fcseed-config and fcseed-sess. The resulting files include: wm.dat, wm.dat.pca-stats.dat and wm.dat.log. How do I interpret the wm.dat.pca-stats.dat file? There are 388 numbered rows (I'm guessing one per acquisition since # of acquisitions is 388?) and five columns. What do the columns represent? Thanks for your help! - Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ___ 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] FSFAST First-Levels: Fast_selxavg3() ERROR
Hi Doug, Just checking up on the error below. __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana [aaf...@mgh.harvard.edu] Sent: Monday, November 16, 2015 2:14 PM To: Freesurfer support list Subject: Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR Yeah sorry, I was rerunning the preproc. Should be there now. __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, November 16, 2015 12:48 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR When I look in hc016/msit/001/ I only see: cfg.txt f.nii mag.dat mag.nii phase.dat phase.nii Have you deleted the previous analysis? On 11/16/2015 11:41 AM, Afzal, Afsana wrote: > Hi Doug, > > Command: selxavg3-sess -s hc016 -analysis > msit.analysis.sm04.b0dc.mni305 -force > Folder: /autofs/space/lilli_002/users/DARPA-FAST > $SUBJECTS_DIR: /autofs/space/lilli_001/users/DARPA-MEG/freesurfs > > The problem might actually lie with preprocessing. > > Just looking at file sizes, the fmcpr.sm4.mni305.2mm.b0dc.nii.gz file > size for hc016 is 471kb, but it's ~46mb for other subjects. The lh and > rh files for hc016 are also pretty small compared to other subjects. > Not sure what's causing this. > > This is the preproc command I used: preproc-sess -s hc016 -surface > fsaverage lhrh -mni305 -fwhm 4 -per-run -fsd msit -nostc -b0dc -force > > Thanks for your help! > > - Afsana > __ > *Afsana Afzal* > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@nmr.mgh.harvard.edu] > *Sent:* Friday, November 13, 2015 5:04 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR > > hmmm, not sure. Can you send me your selxavg3-sess command and the > folder your ran it from and the $SUBJECTS_DIR ? > doug > > On 11/13/15 4:16 PM, Afzal, Afsana wrote: >> Hi, >> >> I'm doing first level analysis in FSFAST and I'm consistently getting >> the following error when running fast_selxavg3(): >> >> Saving to >> /autofs/space/lilli_002/users/DARPA-FAST/hc016/msit/msit.analysis.sm04.b0dc.mni305/rho1mn.sm.nii.gz >> SmoothOnly requested, so exiting now >> >> Found 0 voxels with corrected AR1 > 0.90 >> Whitening >> Attempted to access indedge(0); index must be a positive integer or >> logical. >> >> Error in fast_histeq (line 53) >> if(indedge(end) ~= ny) indedge = [indedge ny]; end >> >> Error in fast_selxavg3 (line 640) >> [edge bincenter binmap] = fast_histeq(nrho1mn.vol(indmask), >> flac0.acfbins); >> >> >> -- >> ERROR: fast_selxavg3() failed\n >> >> >> I'm only getting the error for mni305 (lh and rh analyses are >> completing without a hitch). I have re-preprocessed and attempted to >> run the analysis several times, but without any success. It's not >> clear what the error means or what's causing it. >> >> Thank you for any help, >> >> Afsana >> >> __ >> *Afsana Afzal* >> Clinical Research Coordinator >> Massachusetts General Hospital >> Division of Neurotherapeutics >> Department of Psychiatry: Neurosciences >> 149 13th St, Room 2612 >> Charlestown, MA 02129 >> Phone: 617-643-5129 >> Fax: 617-726-4078 >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___
Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR
Hi Doug, Command: selxavg3-sess -s hc016 -analysis msit.analysis.sm04.b0dc.mni305 -force Folder: /autofs/space/lilli_002/users/DARPA-FAST $SUBJECTS_DIR: /autofs/space/lilli_001/users/DARPA-MEG/freesurfs The problem might actually lie with preprocessing. Just looking at file sizes, the fmcpr.sm4.mni305.2mm.b0dc.nii.gz file size for hc016 is 471kb, but it's ~46mb for other subjects. The lh and rh files for hc016 are also pretty small compared to other subjects. Not sure what's causing this. This is the preproc command I used: preproc-sess -s hc016 -surface fsaverage lhrh -mni305 -fwhm 4 -per-run -fsd msit -nostc -b0dc -force Thanks for your help! - Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, November 13, 2015 5:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR hmmm, not sure. Can you send me your selxavg3-sess command and the folder your ran it from and the $SUBJECTS_DIR ? doug On 11/13/15 4:16 PM, Afzal, Afsana wrote: Hi, I'm doing first level analysis in FSFAST and I'm consistently getting the following error when running fast_selxavg3(): Saving to /autofs/space/lilli_002/users/DARPA-FAST/hc016/msit/msit.analysis.sm04.b0dc.mni305/rho1mn.sm.nii.gz SmoothOnly requested, so exiting now Found 0 voxels with corrected AR1 > 0.90 Whitening Attempted to access indedge(0); index must be a positive integer or logical. Error in fast_histeq (line 53) if(indedge(end) ~= ny) indedge = [indedge ny]; end Error in fast_selxavg3 (line 640) [edge bincenter binmap] = fast_histeq(nrho1mn.vol(indmask), flac0.acfbins); >> -- ERROR: fast_selxavg3() failed\n I'm only getting the error for mni305 (lh and rh analyses are completing without a hitch). I have re-preprocessed and attempted to run the analysis several times, but without any success. It's not clear what the error means or what's causing it. Thank you for any help, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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] FSFAST First-Levels: Fast_selxavg3() ERROR
Yeah sorry, I was rerunning the preproc. Should be there now. __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, November 16, 2015 12:48 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR When I look in hc016/msit/001/ I only see: cfg.txt f.nii mag.dat mag.nii phase.dat phase.nii Have you deleted the previous analysis? On 11/16/2015 11:41 AM, Afzal, Afsana wrote: > Hi Doug, > > Command: selxavg3-sess -s hc016 -analysis > msit.analysis.sm04.b0dc.mni305 -force > Folder: /autofs/space/lilli_002/users/DARPA-FAST > $SUBJECTS_DIR: /autofs/space/lilli_001/users/DARPA-MEG/freesurfs > > The problem might actually lie with preprocessing. > > Just looking at file sizes, the fmcpr.sm4.mni305.2mm.b0dc.nii.gz file > size for hc016 is 471kb, but it's ~46mb for other subjects. The lh and > rh files for hc016 are also pretty small compared to other subjects. > Not sure what's causing this. > > This is the preproc command I used: preproc-sess -s hc016 -surface > fsaverage lhrh -mni305 -fwhm 4 -per-run -fsd msit -nostc -b0dc -force > > Thanks for your help! > > - Afsana > __ > *Afsana Afzal* > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@nmr.mgh.harvard.edu] > *Sent:* Friday, November 13, 2015 5:04 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR > > hmmm, not sure. Can you send me your selxavg3-sess command and the > folder your ran it from and the $SUBJECTS_DIR ? > doug > > On 11/13/15 4:16 PM, Afzal, Afsana wrote: >> Hi, >> >> I'm doing first level analysis in FSFAST and I'm consistently getting >> the following error when running fast_selxavg3(): >> >> Saving to >> /autofs/space/lilli_002/users/DARPA-FAST/hc016/msit/msit.analysis.sm04.b0dc.mni305/rho1mn.sm.nii.gz >> SmoothOnly requested, so exiting now >> >> Found 0 voxels with corrected AR1 > 0.90 >> Whitening >> Attempted to access indedge(0); index must be a positive integer or >> logical. >> >> Error in fast_histeq (line 53) >> if(indedge(end) ~= ny) indedge = [indedge ny]; end >> >> Error in fast_selxavg3 (line 640) >> [edge bincenter binmap] = fast_histeq(nrho1mn.vol(indmask), >> flac0.acfbins); >> >> >> -- >> ERROR: fast_selxavg3() failed\n >> >> >> I'm only getting the error for mni305 (lh and rh analyses are >> completing without a hitch). I have re-preprocessed and attempted to >> run the analysis several times, but without any success. It's not >> clear what the error means or what's causing it. >> >> Thank you for any help, >> >> Afsana >> >> __ >> *Afsana Afzal* >> Clinical Research Coordinator >> Massachusetts General Hospital >> Division of Neurotherapeutics >> Department of Psychiatry: Neurosciences >> 149 13th St, Room 2612 >> Charlestown, MA 02129 >> Phone: 617-643-5129 >> Fax: 617-726-4078 >> >> >> ___ >> 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 -- 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 h
[Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR
Hi, I'm doing first level analysis in FSFAST and I'm consistently getting the following error when running fast_selxavg3(): Saving to /autofs/space/lilli_002/users/DARPA-FAST/hc016/msit/msit.analysis.sm04.b0dc.mni305/rho1mn.sm.nii.gz SmoothOnly requested, so exiting now Found 0 voxels with corrected AR1 > 0.90 Whitening Attempted to access indedge(0); index must be a positive integer or logical. Error in fast_histeq (line 53) if(indedge(end) ~= ny) indedge = [indedge ny]; end Error in fast_selxavg3 (line 640) [edge bincenter binmap] = fast_histeq(nrho1mn.vol(indmask), flac0.acfbins); >> -- ERROR: fast_selxavg3() failed\n I'm only getting the error for mni305 (lh and rh analyses are completing without a hitch). I have re-preprocessed and attempted to run the analysis several times, but without any success. It's not clear what the error means or what's causing it. Thank you for any help, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ___ 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] Extracing values from ces.nii
Ah, I see. But what do the 27307 rows represent and why are there 6 values per row? Thanks, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, November 03, 2015 1:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracing values from ces.nii It should be interpreted as a 2D structure of size 27307*6= 163842 which are the number of vertices in fsaverage On 10/29/2015 11:41 AM, Afzal, Afsana wrote: > Hi, > > I'm trying to extract the contrast values from ces.nii.gz after > first-level analysis. My goal is to average the contrast values for > each voxel across subjects for a given condition and see where an > individual from a separate population falls within the distribution of > contrast values. > > The ces.nii file I'm working with has the following dimension: (27307, > 1, 6, 1), which I interpreted as containing information about 27307 > voxels in a 3D matrix. What does the information in the 6 rows for > each voxel represent? I was expecting to get a single raw b-value for > each voxel. The structure is consistent with sig.nii and t.nii files > as well. > > Thanks for any help, > > Afsana > __ > *Afsana Afzal* > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > ___ > 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 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] Extracing values from ces.nii
Hi, I'm trying to extract the contrast values from ces.nii.gz after first-level analysis. My goal is to average the contrast values for each voxel across subjects for a given condition and see where an individual from a separate population falls within the distribution of contrast values. The ces.nii file I'm working with has the following dimension: (27307, 1, 6, 1), which I interpreted as containing information about 27307 voxels in a 3D matrix. What does the information in the 6 rows for each voxel represent? I was expecting to get a single raw b-value for each voxel. The structure is consistent with sig.nii and t.nii files as well. Thanks for any help, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ___ 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.
