[Freesurfer] Freesurfer 4.20 for recon-all –all, and Freesurfer 5.10 for recon-all -s subjid -qcache? Workaround for a bug in the group statistics for volume?
Hi I have two questions about the Freesurfer recon-all. Can I use Freesurfer 4.20 for recon-all –all, and Freesurfer 5.10 for recon-all -s subjid -qcache? There was also reported a bug in the group statistics for volume in Freesurfer 5.1. Are there any workaround for this error? ___ 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] WM Parcellation - lobe mapping
Hi All, I need to classify WM into different lobes (temporal, parietal, frontal, occipital). I tried to do the lobe mapping using parcellations from wmparc.mgz. http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation My problem is the unsegmented white matter in wmparc.mgz. My understanding is that these unsegmented areas are classified so because they are beyond 5mm from any pre-classified cortex area. My questions: (1) So in order to classify unsegmented WM into lobes, do I need to take each voxel in the unsegmented WM region and then assign it to the closest cortex area to classify it into respective parcellations. Then re-group into lobes. Is this correct? (2) Are there any tailor made function or any other easier way to do this? Is there any easier way to segment WM into lobes directly that I have missed? Thanks, Brain ___ 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] Ventricular structures - exact definitions
Hello, as I am interested in the volume of ventricular structures in the brain, I would like to more precisely understand the labels given by /stats/aseg.stats in Freesurfer. Most importantly, what is the precisely defined difference between Left-Lateral-Ventricle and Left-Inf-Lat-Vent? Would you always combine these two in a volumetric study? Why are they separately segmented? And what exactly is the 5th-Ventricle? Less importantly, how exactly do you define CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior, and CC_Anterior? Is there a paper or homepage defining these exactly? Any help appreciated! Thanks a lot, Meike ___ 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] dcm2nii and recon all
Dear FS' users, I have a 3D T1 from a GE scanner which I convert with dcm2nii to use it with recon-all, but I got 3 images: o -- original oo -- orthogonal co -- cropped image Which I should use to run the command recon-all? thanks! Carolina ___ 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] Longitudinal aseg errors
Hi Jeff, after editing anything in the cross, you usually need to rerun the base (and then all longs). Also you need to edit the base (brainmask, talairach) as that is where the long processes take the information from. It is more important to fix the base than the cross in many cases. More on longitudinal editing is here: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits Examples are in the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial Good luck, Martin On Thu, 2011-09-01 at 10:24 -1000, Jeff Sadino wrote: Hello, I finished processing my first longitudinal subjects, but I have some errors. The TP3.long aseg.mgz file is poorly segmented (corpus callosum, see attachment). I am wondering where I should make edits to correct this. The surfaces of all 3 longitudinal timepoints look fine, so according to the wiki, I should only have to edit the TP3.long. Is that true? If not, then I will have to edit TP3.cross. Originally, the watershed for TP3.cross was bad. I edited this and re-ran autorecon2 and autorecon3, and exited with no errors. However, the cross aseg.mgz is still bad. I thought maybe the talairach.m3z file was bad, but the nu_noneck image was transformed fine. I see that the log file says during the mri_ca_label step that the CSF peak is too bright - rejecting (see attachment). After comparing the csf areas of the TP3.cross norm image with the csf areas of the TP1.cross norm image, they have values of 30 compared to values of 10. Previous posts have suggested to copy the orig.mgz image to the nu.mgz image for a similar problem. Can someone please advise me on where it would be best to make the edits so that my longitudinal reconstructions are accurate? Thank you! Jeff Sadino ___ 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] what is thalamus-proper and clusters-table related question
Dear FS list, 1. What does a label Thalamus Proper include? Is it the same as thalamus? 2. After correcting for multiple comparisons, I get a table of clusters. I have several questions regarding this table: What do the columns Max, CWPLow, and CWPHigh represent? Regarding the NVtxs column: is it the number of vertexes in cluster? What kind of information can I get from this value? If two clusters have different areas but the same number of vertexes, does it mean something? Thank you very much for your help and for your time, Tanja. ___ 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] what is thalamus-proper and clusters-table related question
I'm not sure about #1, maybe BF can chime in. Tetiana Dadakova wrote: Dear FS list, 1. What does a label Thalamus Proper include? Is it the same as thalamus? 2. After correcting for multiple comparisons, I get a table of clusters. I have several questions regarding this table: What do the columns Max, CWPLow, and CWPHigh represent? 1. CWP - cluster-wise pvalue. The pvalue of the cluster corrected for multiple comparisons 2. CWPLow - lower 90% confidence limit of CWP based on binomial distribution 3. CWPHi - upper 90% confidence limit of CWP based on binomial distribution Regarding the NVtxs column: is it the number of vertexes in cluster? Yes What kind of information can I get from this value? It is not very informative so don't feel like you have to use it. It is good for assuring that the software is doing the right thing. If two clusters have different areas but the same number of vertexes, does it mean something? It means that the area of the component triangles that make up the vertices is different. doug Thank you very much for your help and for your time, Tanja. ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] dcm2nii and recon all
I have no idea, but probably the original. doug Carolina Valencia wrote: Dear FS' users, I have a 3D T1 from a GE scanner which I convert with dcm2nii to use it with recon-all, but I got 3 images: o -- original oo -- orthogonal co -- cropped image Which I should use to run the command recon-all? thanks! Carolina ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Grad_Unwarp question
The grad_unwarp_tables directory is not distributed with the public release of freesurfer, as the files are under Siemens license to the NMR Center only. So I suppose you could check with Siemens to see if they can supply you with those data tables for your scanner. N. Hello, We used to run: grad_unwarp with matlab invoked with -nodisplay option. The version information on this file is: version: Version for distribution, 1.0, author: SC--- id: id9/01 13:34:11 I see that Freesurfer 5.1 has a grad_unwarp script, which I can modify to invoke matlab with -nodisplay, however, I dont see any sub-folder grad_unwarp_tables in FREESURFER_HOME. Where do I get these tables from? Am I missing some installation option? Regards Mohana ___ 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] what is thalamus-proper and clusters-table related question
Actually I have the same question - does the thalamus proper include LGN ? - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Tetiana Dadakova tetian...@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 2, 2011 12:28:45 PM Subject: Re: [Freesurfer] what is thalamus-proper and clusters-table related question I'm not sure about #1, maybe BF can chime in. Tetiana Dadakova wrote: Dear FS list, 1. What does a label Thalamus Proper include? Is it the same as thalamus? 2. After correcting for multiple comparisons, I get a table of clusters. I have several questions regarding this table: What do the columns Max, CWPLow, and CWPHigh represent? 1. CWP - cluster-wise pvalue. The pvalue of the cluster corrected for multiple comparisons 2. CWPLow - lower 90% confidence limit of CWP based on binomial distribution 3. CWPHi - upper 90% confidence limit of CWP based on binomial distribution Regarding the NVtxs column: is it the number of vertexes in cluster? Yes What kind of information can I get from this value? It is not very informative so don't feel like you have to use it. It is good for assuring that the software is doing the right thing. If two clusters have different areas but the same number of vertexes, does it mean something? It means that the area of the component triangles that make up the vertices is different. doug Thank you very much for your help and for your time, Tanja. ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Surface analysis FSL GFEAT results for multiple subjects with 4 runs each
Hi Freesurfers, I've been looking at the wiki for information on doing an surface analysis using GFEAT results for within subject, across multiple runs. On the wiki, a fixed effects analysis was used because there were only two runs. I have four runs and FSL uses FLAME 1 and FLAME 1+2. 1. Should/how do I do I random effects for 4 runsb? 2. How does one do a group surface analysis this for multiple subjects who each have 4 runs? Thanks. Michelle ___ 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] what is thalamus-proper and clusters-table related question
Yes, not sure why the CMA called it that On Sep 2, 2011, at 12:28 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I'm not sure about #1, maybe BF can chime in. Tetiana Dadakova wrote: Dear FS list, 1. What does a label Thalamus Proper include? Is it the same as thalamus? 2. After correcting for multiple comparisons, I get a table of clusters. I have several questions regarding this table: What do the columns Max, CWPLow, and CWPHigh represent? 1. CWP - cluster-wise pvalue. The pvalue of the cluster corrected for multiple comparisons 2. CWPLow - lower 90% confidence limit of CWP based on binomial distribution 3. CWPHi - upper 90% confidence limit of CWP based on binomial distribution Regarding the NVtxs column: is it the number of vertexes in cluster? Yes What kind of information can I get from this value? It is not very informative so don't feel like you have to use it. It is good for assuring that the software is doing the right thing. If two clusters have different areas but the same number of vertexes, does it mean something? It means that the area of the component triangles that make up the vertices is different. doug Thank you very much for your help and for your time, Tanja. ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] what is thalamus-proper and clusters-table related question
I dint think it does, but maybe jean or David can confirm On Sep 2, 2011, at 1:07 PM, Ritobrato Datta rida...@mail.med.upenn.edu wrote: Actually I have the same question - does the thalamus proper include LGN ? - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Tetiana Dadakova tetian...@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 2, 2011 12:28:45 PM Subject: Re: [Freesurfer] what is thalamus-proper and clusters-table related question I'm not sure about #1, maybe BF can chime in. Tetiana Dadakova wrote: Dear FS list, 1. What does a label Thalamus Proper include? Is it the same as thalamus? 2. After correcting for multiple comparisons, I get a table of clusters. I have several questions regarding this table: What do the columns Max, CWPLow, and CWPHigh represent? 1. CWP - cluster-wise pvalue. The pvalue of the cluster corrected for multiple comparisons 2. CWPLow - lower 90% confidence limit of CWP based on binomial distribution 3. CWPHi - upper 90% confidence limit of CWP based on binomial distribution Regarding the NVtxs column: is it the number of vertexes in cluster? Yes What kind of information can I get from this value? It is not very informative so don't feel like you have to use it. It is good for assuring that the software is doing the right thing. If two clusters have different areas but the same number of vertexes, does it mean something? It means that the area of the component triangles that make up the vertices is different. doug Thank you very much for your help and for your time, Tanja. ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Regarding Segmentation of Hippocampal Subfield
Hello, When I segmented the Hippocampal Subfields (using the process stated in http://www.freesurfer.net/fswiki/HippocampalSubfieldSegmentation ) it generated two files by name *posterior_Left-Hippocampus.mgz* and * posterior_Right-Hippocampus.mgz*. I would like to know what actually are those since they are not actual Hippocampus. When I am generating the crisp images do I need to use those files also, if so what are the labels of those regions. Also, what about the *right_alveus, right_fornix, left_alveus, left_fornix*regions. They haven't generated in the segmentation. Is there a way to generate those regions also. Any help regarding would be appreciated. Thank you. -- With Thanks Regards, Mohan Boddu ___ 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] what is thalamus-proper and clusters-table related question
I don't think it does. Jean manually labeled LGN in a few cases for me a few years ago, and I vaguely remember that LGN did not overlap with our thalamus seg (but I could be wrong). doug Bruce Fischl wrote: I dint think it does, but maybe jean or David can confirm On Sep 2, 2011, at 1:07 PM, Ritobrato Datta rida...@mail.med.upenn.edu wrote: Actually I have the same question - does the thalamus proper include LGN ? - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Tetiana Dadakova tetian...@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 2, 2011 12:28:45 PM Subject: Re: [Freesurfer] what is thalamus-proper and clusters-table related question I'm not sure about #1, maybe BF can chime in. Tetiana Dadakova wrote: Dear FS list, 1. What does a label Thalamus Proper include? Is it the same as thalamus? 2. After correcting for multiple comparisons, I get a table of clusters. I have several questions regarding this table: What do the columns Max, CWPLow, and CWPHigh represent? 1. CWP - cluster-wise pvalue. The pvalue of the cluster corrected for multiple comparisons 2. CWPLow - lower 90% confidence limit of CWP based on binomial distribution 3. CWPHi - upper 90% confidence limit of CWP based on binomial distribution Regarding the NVtxs column: is it the number of vertexes in cluster? Yes What kind of information can I get from this value? It is not very informative so don't feel like you have to use it. It is good for assuring that the software is doing the right thing. If two clusters have different areas but the same number of vertexes, does it mean something? It means that the area of the component triangles that make up the vertices is different. doug Thank you very much for your help and for your time, Tanja. ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] dcm2nii and recon all
I am also using dcm2nii and running recon-all with the original image. It is working ok so far. Alfredo Date: Fri, 2 Sep 2011 12:30:26 -0400 From: gr...@nmr.mgh.harvard.edu To: cvalen...@linkdx.com.co CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] dcm2nii and recon all I have no idea, but probably the original. doug Carolina Valencia wrote: Dear FS' users, I have a 3D T1 from a GE scanner which I convert with dcm2nii to use it with recon-all, but I got 3 images: o -- original oo -- orthogonal co -- cropped image Which I should use to run the command recon-all? thanks! Carolina ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
